Inclusion of ENCORE into MDAnalysis#797

Merged

richardjgowers merged 124 commits intoMDAnalysis:developfrom

encore-similarity:feature-encore

Oct 12, 2016

Commits on Feb 11, 2016

Commits on Feb 16, 2016

updated documentation and codestyle
tbengtsen
committed

Commits on Feb 18, 2016

fixed conf. dist. matrix bug in dres and refactored similarity_mode options
mtiberti
committed
Added Encore unit-tests
Wouter Boomsma
committed

Commits on Feb 19, 2016

Commits on Feb 20, 2016

fixed load_matrix bug
mtiberti
committed
Fixed Encore unit tests in response to API change.
Wouter Boomsma
committed

Commits on Feb 22, 2016

Commits on Mar 2, 2016

Commits on Mar 4, 2016

Commits on Mar 8, 2016

Commits on Mar 9, 2016

Added unit tests for ArrayReader
Wouter Boomsma
committed

Commits on Mar 10, 2016

edited documentation
mtiberti
committed

Commits on Mar 11, 2016

Minor bugfix in ArrayReader
Wouter Boomsma
committed
Merge branch 'develop' of https://github.com/encore-similarity/mdanalysis into develop
Wouter Boomsma
committed

Commits on Mar 14, 2016

Commits on Mar 15, 2016

removed useless is_int function
mtiberti
committed

Commits on Mar 17, 2016

Increased test coverage of Ensemble.py and array.py
Wouter Boomsma
committed

Commits on Mar 21, 2016

Commits on Mar 22, 2016

Increased test coverage in encore.
Wouter Boomsma
committed
added test
mtiberti
committed

Commits on Mar 23, 2016

Removed topology_filename attribute from Ensemble class.
Wouter Boomsma
committed
Removed __iter__ from ArrayReader.
Wouter Boomsma
committed

Commits on Mar 24, 2016

Commits on Apr 2, 2016

ArrayReader renamed to MemoryReader
Wouter Boomsma
committed

Commits on Apr 3, 2016

Removed Ensemble class
Wouter Boomsma
committed

Commits on Apr 4, 2016

Simplified coordinate extraction code in Universe.transfer_to_memory
Wouter Boomsma
committed
Added dimensions and dt support to MemoryReader.
Wouter Boomsma
committed
Changed dict.iteritems() to six.iteritems(dict)
mtiberti
committed
changed numpy.array to numpy.asarray to avoid making useless copies
mtiberti
committed
defaulted number of cores to 1 in confdistmatrix
mtiberti
committed
Bugfix in coordinate extraction in Universe.transfer_to_memory().
Wouter Boomsma
committed
Removed check for empty selection string in Universe.select_atoms()
Wouter Boomsma
committed
numpy -> np in covariance.py
Wouter Boomsma
committed

Commits on Apr 5, 2016

Removed call to np.cov in covariance.py - ML case.
Wouter Boomsma
committed
Added special case in Selection.AllSelection to speed up "all" selections.
Wouter Boomsma
committed

Commits on Apr 7, 2016

Changed slice convention in MemoryReader to follow that of numpy.
Wouter Boomsma
committed

Commits on Apr 8, 2016

removed debug print statement
mtiberti
committed

Commits on Apr 15, 2016

Changed behavior so clusters are returned even when not fully converged (warning is issued).
Wouter Boomsma
committed

Commits on Apr 26, 2016

removed debug prints
mtiberti
committed

Commits on Apr 29, 2016

cosmetical changes
mtiberti
committed

Commits on May 3, 2016

Merge branch 'feature-encore' of https://github.com/encore-similarity/mdanalysis into feature-encore
mtiberti
committed

Commits on May 9, 2016

Commits on May 20, 2016

moved cython/c file according to the new paradigm and modified setup.py accordingly
mtiberti
committed

Commits on May 23, 2016

Commits on May 25, 2016

Encore: Adjusted expected results for hes tests: test failures were due to minor bug in previous version.
Wouter Boomsma
committed

Commits on Aug 15, 2016

Code reorganization, cleanup and bugfixes.
Wouter Boomsma
committed
Added cluster.py
Wouter Boomsma
committed

Commits on Aug 18, 2016

streamlined convergence functions
mtiberti
committed

Commits on Sep 3, 2016

Commits on Sep 6, 2016

Decreased sensitivity of hes_align test.
Wouter Boomsma
committed
Added missing warnings import
Wouter Boomsma
committed
Fixed test_reader_w_timeseries_frame_interval test
Wouter Boomsma
committed
Bugfix in similarity.py
Wouter Boomsma
committed
Added sklearn as optional requirement in setup.py and .travis.yml. Minor bugfixes.
Wouter Boomsma
committed
Minor corrections to MemoryReader code, tests and documentation.
Wouter Boomsma
committed
Removed debugging print statements.
Wouter Boomsma
committed

Commits on Sep 7, 2016

sklearn -> scikit-learn in setup.py
Wouter Boomsma
committed
Added missing warnings import
Wouter Boomsma
committed
Added sklearn availability tests to two tests.
Wouter Boomsma
committed
Fixed QuantitiveCode issues. Added sklearn availability tests to several tests.
Wouter Boomsma
committed
Fixed QuantitiveCode issue
Wouter Boomsma
committed
Changed ParallellCalculation to run in main thread when ncores==1. Added tests.
Wouter Boomsma
committed

Commits on Sep 8, 2016

Inreased travis process timeout to 400s
Wouter Boomsma
committed

Commits on Sep 9, 2016

Speeded up tests. Reverted back to 300s process timeout. Bugfix in hes error estimation.
Wouter Boomsma
committed
Removed obsolete code.
Wouter Boomsma
committed
Removed debugging print statements
Wouter Boomsma
committed
Increased robustness of test
Wouter Boomsma
committed

Commits on Sep 10, 2016

Inreased travis process timeout to 400s
Wouter Boomsma
committed
Added documentation, and removed unused import
Wouter Boomsma
committed

Commits on Sep 11, 2016

Commits on Sep 13, 2016

first pass on documentation
mtiberti
committed

Commits on Sep 14, 2016

revised tests in documentation
mtiberti
committed

Commits on Sep 15, 2016

Extra documentation and minor bugfix
wouterboomsma
committed

Commits on Sep 16, 2016

Merge remote-tracking branch 'upstream/develop' into feature-encore
mtiberti
committed

Commits on Sep 20, 2016

Commits on Sep 28, 2016