modified:   jt
- Made path argument in calls like 'jt run /my/pipeline' optional. By default,
  will use current working directory as an the pipeline path.
modified:   jterator/module.py
- Fixed: removed a leftover assigment to self.streams['error] in
  set_standard_output()
- Refactored writing logs into a separate method.

modified:   tests/mock/foo_example/modules/foo.py
modified:   tests/mock/foo_example/modules/foo.py
- Commented the line provoking the test to fail.
new file:   tests/mock/jterator
- A relative symbolic link - to simplify imports.
new file:   jterator/api/__init__.py
new file:   jterator/api/io.py
modified:   jterator/module.py
- Refactoring API functions that help users to develop modules into a separate
  namespace called jterator.api.*
new file:   .travis.yml
- Integration with Travis (for continuous "integration")
new file:   setup.py
- Adding setuptools support
- Registering package on PyPI
modified:   README.md
- Added travis status button.
modified:   setup.py
- Lowering requirements for h5py to 2.2.1
modified:   ../.travis.yml
modified:   ../README.md
modified:   ../setup.py
- Improving dependencies from h5py for travis builds.
modified:   README.md
- Minor rewrite.
modified:   jterator/api/__init__.py
- Exposed h5py as h5. Now one can do: import jterator.api.h5
modified:   setup.py
- Minor changes
modified:   .travis.yml
- calls silent nosetests (no capture plugin which is on by default).

new file:   Makefile
- Added a better `make clean`

new file:   jterator/tree_output.py
- Adding new module to help visualize progress of JteratorRunner. Supports
  JSON, ASCII, ANSI and NULL outputs.

modified:   setup.py
- Modified and fixed wrong arguments in setup().

new file:   tests/mock/expected_ansi
new file:   tests/test_tree_output.py
- Tests for HierarchicalOutput() instances.
modified:   setup.py
- Weakend the requirement for h5py as >= 2.2.1
modified:   .gitignore
- ignoring mock example logs in tests
Merge branch 'upstream_master'

Conflicts:
	jterator/module.py
-- Moved/updated code to jterator.api.io module.
new file:   TODO
modified:   TODO
deleted:    jterator/__init__.py
modified:   setup.py
renamed:    jterator/+module_m/h5attget.m -> src/matlab/+jterator/+api/+h5/h5attget.m
renamed:    jterator/+module_m/h5attput.m -> src/matlab/+jterator/+api/+h5/h5attput.m
renamed:    jterator/+module_m/h5datacreate.m -> src/matlab/+jterator/+api/+h5/h5datacreate.m
renamed:    jterator/+module_m/h5varget.m -> src/matlab/+jterator/+api/+h5/h5varget.m
renamed:    jterator/+module_m/h5varput.m -> src/matlab/+jterator/+api/+h5/h5varput.m
renamed:    jterator/+module_m/check_input_args.m -> src/matlab/+jterator/+api/+io/check_input_args.m
renamed:    jterator/+module_m/get_handles.m -> src/matlab/+jterator/+api/+io/get_handles.m
renamed:    jterator/+module_m/read_input_args.m -> src/matlab/+jterator/+api/+io/read_input_args.m
renamed:    jterator/+module_m/write_output_args.m -> src/matlab/+jterator/+api/+io/write_output_args.m
renamed:    jt -> src/python/jt
new file:   src/python/jterator/__init__.py
renamed:    jterator/api/__init__.py -> src/python/jterator/api/__init__.py
renamed:    jterator/api/io.py -> src/python/jterator/api/io.py
renamed:    jterator/error.py -> src/python/jterator/error.py
renamed:    jterator/minify_json.py -> src/python/jterator/minify_json.py
renamed:    jterator/module.py -> src/python/jterator/module.py
renamed:    jterator/runner.py -> src/python/jterator/runner.py
renamed:    jterator/tree_output.py -> src/python/jterator/tree_output.py
renamed:    jterator/utils.py -> src/python/jterator/utils.py
new file:   src/r/DESCRIPTION
renamed:    jterator/module_r/h5readatt.R -> src/r/h5readatt.R
deleted:    tests/jterator
- Separated code per language.
- Also substructured core code and api code. Each language has it own packaging
  system, so we will have to adhere individually and package api accordingly.
  Only python package contains the core code, i.e. jt command-line utility.
  What is important is to maintain similar object/package structure layout, e.g.

    jterator.api.io - package will contain respective functions in all languages.
Merge pull request #3 from ewiger/master

A working layout of Jterator pipelines