Changes to be committed:
Changes to be committed:
Merge branch 'master' of https://github.com/ewiger/Jterator
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.
Changes to be committed:
-renamed:    ExampleProject/JHandles_ExampleProject.h5 -> ExampleProject/ExampleProject.h5
-new file:   ExampleProject/ExampleProject.pipe
-deleted:    ExampleProject/JPipe_ExampleProject.json
-new file:   ExampleProject/JT/input/read_filenames.handles
-new file:   ExampleProject/JT/modules/jterator
-new file:   ExampleProject/JT/modules/read_filenames.jt
-modified:   README.md
-modified:   example/modules/foo.py
-new file:   jterator/module.py
modified:   jt
- Calling Jterator() in cli.run() to build and execute the pipeline.
Changes to be committed:
	new file:   module.m
        - handling of standard input as JSON and of input and output arguments of a module similar to the implementation in module.py
Changes to be committed:
	new file:   +module_m/get_handles.m
	new file:   +module_m/read_input_args.m
	new file:   +module_m/write_output_args.m
    - reorganization of the matlab code -> package containing individual functions
Changes to be committed:
	deleted:    module.m
    - now as package +module_m
Changes to be committed:
	new file:   illum_correct.jt
    - example Matlab module
Changes to be committed:
	modified:   illum_correct.jt
    - example matlab module with input checks via inputParser
	modified:   ../../../jterator/+module_m/read_input_args.m
    - editing
Changes to be committed:
	modified:   illum_correct.jt
    - input arguments for function are specified in the documentation part of the function in JSON, which could be read and written into the .pipe file
    (maybe even automatically to produce a skeleton of the pipeline).
Changes to be committed:
	modified:   illum_correct.jt
    - adaptations described in previous commit (JSON specifying input and output arguments in the documentation of the module) were placed in better position, namely directly at the beginning of the module
Changes to be committed:
	modified:   illum_correct.jt
    - correction of JSON syntax in documentation (see previous commit)
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.