Add release notes for v0.7.1 (brainiak#340)

Add release notes for v0.7 (brainiak#333)

Add release notes for v0.6 (brainiak#297)

docs: Cite all references (brainiak#226)

Fixes warnings introduced in Spinx 1.6.1:
sphinx-doc/sphinx#3565

[fmrisim] Improve simulator (brainiak#150)

* Add TDA initial script.

* Added documentation

* Added documentation

* Added documentation

* Added the test_tda

* Simulator initial commit. Includes the simulator function with the tests and examples

* Error in uploading simulator

* Updated simulator based on edits. Added two condition example. Removed TDA code.

* Updated names, improved comments, changed load procedure for mask

* Updated simulator

* Updated the way TDA features are generated

* Updated tests for new simulator code

* Updated fmrisim test, corrected error of deleting test_hpo

* No need to make any change to hyperparamopt

* Updated doc string

* Conforming to PEP8

* Removed nibabel

* Increased test coverage

* Updated for PEP8

* Updated for pep8

* Updated for pep8

* Updated pep8

* Edited the tests

* Complexity tests updating

* Updated tests

[reprsimil] Mostly bug fixing for brsa (brainiak#144)

* a
 Changes to be committed:
	new file: brainiak/brsa/test.txt

* 	deleted:    brsa/test.txt

* changed some of the logging levels

* Creating new functions to prepare to a new version which explicitly deals with shared time series not explained by design matrix

* Further changing singpara, preparing to deal with shared time series X0

* Changed the model to consider spatial correlation in noise

* Updated the BRSA model to incorporate spatial correlation in noise
Fixed some bugs in utils.ReadDesign
Renamed epsilon to eta in consistence with the paper
Expanded the example a bit
Other minor changes

* fixed some bugs and typos

* Removed some redundant calculation"

* changed some of the logging levels

* Creating new functions to prepare to a new version which explicitly deals with shared time series not explained by design matrix

* Further changing singpara, preparing to deal with shared time series X0

* Changed the model to consider spatial correlation in noise

* attempt to solve conflict

 Changes to be committed:
	modified:   brainiak/reprsimil/brsa.py
	modified:   brainiak/utils/utils.py
	modified:   examples/reprsimil/brsa_representational_similarity_estimate_example.ipynb
	modified:   tests/reprsimil/test_brsa.py
	modified:   tests/utils/test_utils.py

* fixed some bugs and typos

* Removed some redundant calculation"

* Removing some unnecessary package in brsa example

* adding comment on nuisance regressor

* removing outdated note in brsa

* updating docstring

* a bit more changing of docstring

* minor changes

* update the example for brsa

* updating example to do z-scoring

* cleaning up

* cleaning up

* fix a bug in utils.ReadDesign

* bug fixing for BRSA._prepare_data_XYX0

* trivial

* changes re PR review

Merge pull request brainiak#124 from TuKo/semiexample

Corrected SS-SRM example

Semi-Supervised SRM code (brainiak#108)

* Added Semi-Supervised SRM

* Resolved function complexity check

* remove the verbose flag

* Remove verbose flag from test

* Added test for data fit of the model

* Removed the  verbose flag from example.

* modify 20 by INFO constant

* added logging to test to include missing coverage

* Corrected minor doc errors

* modified pr-check for theano correct testing

* Divided tests

* Modified documentations

* Modified cost by alpha

* Corrected the test for one utility function

Merge pull request brainiak#89 from mihaic/release-v0.2

Update version to 0.2

Merge pull request brainiak#59 from mihaic/v0.1

Various fixes for v0.1