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VAMP estimator and cktest #1237

Merged
merged 44 commits into from Feb 7, 2018
Merged

VAMP estimator and cktest #1237

merged 44 commits into from Feb 7, 2018

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marscher
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@marscher marscher commented Feb 5, 2018

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Paul, Fabian (fapa) and others added 27 commits February 4, 2018 12:30
@marscher
implement VAMP
bae12a3
@marscher
w.i.p
e1adf94
@marscher
w.i.p
23a2e35
@marscher
w.i.p
83ed063
@marscher
[vamp] update docs, names
6f98bf8
@marscher
[vamp] implement CK test
61b1f14
@marscher
[vamp] CK-test now returns LaggedModelValidator
359f406
@marscher
[vamp] more progressbar tweaking/debugging
da01344
@marscher
[vamp] w.i.p. to make future-proof for serializable estimators/models
53b7097
@marscher
[vamp] new unit test: test against MSM without removal of data mean
d7275f2
@marscher
[vamp] drafted implementation of scores, w.i.p
c29affd
@marscher
[vamp] fix error in unit test
7aefe99
@marscher
[vamp] drafted unit test for scores
63f4307
@marscher
scoring changes:
492d191 
* moved diagonalization method to model
* Added score test
* made signatures of score method analog to MSM
@marscher
[msm] fix parameter type in docstring
b6a4776
@marscher
fixed tests, moved lazy estimation to model
23b5573
@marscher
[vamp] bugfixes
1d74319
@marscher
updated to devel, made serializable, removed obsolete hacks.
7def433
@marscher
documentation [ci skip]
28f3622
@marscher
merged devel
518d723
@marscher
[coor/api] string types usage, chunksize
c2ca705
@marscher
fix merge mistakes
6a717c4
@marscher
revert (eps defined)
9d0892c
@marscher
[doc] amend changelog
ba3d673
@marscher
revert absolute import removal
182ba9b
@marscher
minor
48d2c31
@marscher
[lagged covar] properly deprecate chunksize arg.
3aee7e7
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codecov bot commented Feb 5, 2018 •
edited

Codecov Report

Merging #1237 into devel will increase coverage by 0.12%.
The diff coverage is 93.03%.

Impacted file tree graph

@@            Coverage Diff             @@
##            devel    #1237      +/-   ##
==========================================
+ Coverage   91.03%   91.16%   +0.12%     
==========================================
  Files         217      219       +2     
  Lines       23072    23558     +486     
==========================================
+ Hits        21003    21476     +473     
- Misses       2069     2082      +13
Impacted Files Coverage Δ
pyemma/coordinates/__init__.py 100% <ø> (ø) ⬆️
pyemma/msm/estimators/maximum_likelihood_msm.py 88.63% <ø> (+0.35%) ⬆️
pyemma/coordinates/acf.py 82.69% <ø> (-0.33%) ⬇️
pyemma/util/annotators.py 74.32% <ø> (+1.35%) ⬆️
pyemma/msm/estimators/lagged_model_validators.py 78.73% <100%> (+0.5%) ⬆️
pyemma/util/_config.py 82.32% <100%> (+0.87%) ⬆️
pyemma/msm/estimators/__init__.py 100% <100%> (ø) ⬆️
pyemma/_base/estimator.py 89.41% <100%> (+2.11%) ⬆️
pyemma/coordinates/data/util/reader_utils.py 90.26% <100%> (-0.09%) ⬇️
pyemma/msm/estimators/maximum_likelihood_hmsm.py 86.04% <100%> (+0.06%) ⬆️
... and 24 more

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@marscher
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marscher commented Feb 5, 2018

I removed those merge commits which deleted absolute imports (important for py27 backward compat). Now the PR is is much more readable. Any volunteers to review this?

marscher and others added 16 commits February 5, 2018 19:09
@marscher
[test-vamp] compare partial_fit output with a numerical tol of 1e-15
b682e7f
@marscher
[test-vamp] compare only 2 significant digits vs. MSM score for VAMPE
18d2d3b
@marscher
lower tol, fix codacy hint.
de69bf1
@marscher
fix some codacy issues.
6ad85e6
@marscher
fix py2 issue (missing exception)
1c1570f
@marscher
windoze sissy
4a2568e
@marscher
use assert_allclose_ingore_phase for partial_fit test
c68c1bd
@marscher
[test-vamp] compare projected trajs phase agnostic.
73bfd63
@marscher
[vamp] swapped observables, statistics arg to be consistent.
886c19d 
removed obsolete todos
added doc strings
@marscher
fix argument order
5d6f4d3
[vamp] add documentation
95c2321
Merge branch 'vamp_rebased' of https://github.com/marscher/PyEMMA int…
9486937 
…o vamp_rebased
[vamp] docstrings
c0a6395
[vamp] corrected docstrings
92d59d7
[vamp] fix equations in docstring
dd11151
[vamp] vamp.dimension depends on rank of C00 and C11
2fb9d9a
@marscher marscher merged commit 4173ebe into markovmodel:devel Feb 7, 2018
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