Merge remote-tracking branch 'upstream/master' into fix/reporting

* upstream/master:
  fixed more bugs
  fixed doctests
  fixed refit
Merge remote-tracking branch 'upstream/master' into fix/reporting

* upstream/master:
  Fixed typos and paths
fix: updating internal prov to upstream master
enh: adding coveralls
enh: adding coveralls
fix: missing component of travis config
fix: simplify coverage call
fix: testing coverall configuration
fix: limit text literal in provenance to 1MB
Merge branch 'master' into fix/reporting

* master:
  fix: updated doctest, pep8 and unit test
  doc: updated doctest to use literal string
  fix: display cmdline string explicitly
  tst: added test_fslmerge with check for tr updates
  rf: modify fsl.Merge api to abstract setting TR when merging along time dimension
  fix: indentation error
  fix: include name_source and name_template for mergefile in fsl.Merge input_spec
  add: _format_arg override to support tr
  rm: _list_outputs and _gen_filename from fsl.Merge
  doc: updated to use funcfile and test cmdline output
  fix: set tr position to -1
  add: option 'a' for autochoose
  tst: included tr in test dict for fsl.Merge
  doc: improved for fsl.Merge and included example usage
  add: support for setting TR in fsl.Merge
  Add FSFAST option to RapidArt
enh: added coveralls support
sty: pep8 and metadata fixes
doc: include travis and coveralls badges
Merge pull request #709 from satra/fix/reporting

few more updates including coveralls support
fix: remove deprecation warning.
sty: remove commented interface
enh: modified checkspecs to write input spec tests
enh: modified checkspecs to write output spec tests
tst: added autogenerated input and output spec tests
fix: update test generator to take manual edits into account