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Diffusion Map Refactor/Implementation #863

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c511ead
new analysis feature: diffusion map
Mar 2, 2016
3be892e
description of diffusion map
Mar 2, 2016
3ce705a
diffusionmap minor fix
Mar 2, 2016
328c27a
test for diffusionmap
Mar 2, 2016
d2d4593
diffusionmap faster test
Mar 2, 2016
ed5f4c5
included notes
Mar 11, 2016
2947c0f
initial work for refactor
jdetle May 24, 2016
7e94a58
functional refactor
jdetle May 24, 2016
ab7f93c
updated changes
jdetle May 24, 2016
43144e0
iteration error
jdetle May 29, 2016
18c84ee
refactor of @euhruska diffusion map
jdetle May 29, 2016
0da96fa
removed deco import
jdetle May 29, 2016
2c93f2d
added tests, fixed logger issue
jdetle May 30, 2016
49578a0
style fixes, protection fixes, added docs
jdetle Jun 3, 2016
7ec486a
fix of some broken areas
jdetle Jun 3, 2016
f350eaa
small docs fix
jdetle Jun 4, 2016
245d2e8
Constant epsilon tests
jdetle Jun 6, 2016
17fced2
updated CHANGELOG
jdetle Jun 6, 2016
14b08e4
fixed selections and updated tests accordingly
jdetle Jun 8, 2016
cfcbfe0
switched order of imports [skip ci]
jdetle Jun 8, 2016
07a83d1
Separated calculation of distance matrix from diffusion
jdetle Jun 10, 2016
6faec56
Working refactor
jdetle Jun 10, 2016
48c27a9
Change of direction in API, more work to be done implementing everything
jdetle Jun 16, 2016
fe08866
added timescaling, fixed some parts
jdetle Jun 16, 2016
cafeb68
Automodule added, Changed some object oriented stuff around
jdetle Jun 16, 2016
bb394ec
Changed things around to get embedding working
jdetle Jun 16, 2016
074a950
Docs fixes
jdetle Jun 17, 2016
68f2928
Added tests, found bugs, squashed bugs.
jdetle Jun 17, 2016
98e899b
Eliminated square of distance, random mistake
jdetle Jun 17, 2016
b893244
Now witness the firepower of this fully armed and
jdetle Jun 18, 2016
7b12ece
Satisfying the linter
jdetle Jun 18, 2016
e5a3487
Updated docs
jdetle Jun 18, 2016
cbf685d
Fixed bug in _single_frame()
jdetle Jun 19, 2016
e0ed7b4
Eliminated spectral gap function... for now
jdetle Jun 21, 2016
303b816
Fixed matrix multiplication bug
jdetle Jun 23, 2016
01dc0d5
Better single_frame loop
jdetle Jun 27, 2016
2f2db09
Refactor of code to stop DiffusionMap inheriting from AnalysisBase
jdetle Jun 29, 2016
34b1e7c
Removed epsilon class from pull request, now must supply a constant a…
jdetle Jun 29, 2016
7c56863
Added exception to be thrown for large distance matrices.
jdetle Jun 29, 2016
bd40f38
Updated diffusion map after some test-driven development, added error…
jdetle Jun 29, 2016
420edd0
Fixed some docs [skip ci]
jdetle Jun 30, 2016
c058c6c
Change to warning
jdetle Jun 30, 2016
b6c309a
Updated CHANGELOG
jdetle Jun 30, 2016
8ba1a58
Fixes as suggested to be more pythonic and elegant
jdetle Jul 1, 2016
aa22772
Fixes to docs, Transform function.
jdetle Jul 3, 2016
97c3105
Removed anisotropic kernel creation. Figured out that I was
jdetle Jul 3, 2016
b3b2ce9
Small style change
jdetle Jul 5, 2016
c5d1958
Updated docs to remove references to anisotropy, update tutorial [ski…
jdetle Jul 5, 2016
d7cd454
Added link to jupyter notebook [skip ci]
jdetle Jul 6, 2016
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updated CHANGELOG
jdetle committed Jun 30, 2016
commit 17fced2171914d8e5870323c9f89e26164e59da5
6 changes: 4 additions & 2 deletions package/CHANGELOG
Original file line number Diff line number Diff line change
@@ -13,7 +13,7 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
??/??/16 kain88-de,jdetle, fiona-naughton, richardjgowers
??/??/16 kain88-de, fiona-naughton, richardjgowers, jandom, euhruska, jdetle
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why does @jandom stand in the authors now?

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I have absolutely no idea 😓


* 0.15.1

@@ -27,7 +27,9 @@ Changes
* Added protected variable _frame_index to to keep track of frame iteration
number in AnalysisBase
* Added new AlignTraj class for alignment that follows the new analysis API known
as Bauhaus style.
as Bauhaus style. (Issue #845)
* Added new diffusionmap module for dimension reduction that follows the
Bauhaus API. (Issue #857)

Deprecations (Issue #599)
* Use of rms_fit_trj deprecated in favor of AlignTraj class (Issue #845)
2 changes: 0 additions & 2 deletions testsuite/MDAnalysisTests/analysis/test_diffusionmap.py
Original file line number Diff line number Diff line change
@@ -57,7 +57,6 @@ def test_weights(self):
dmap2.run()
assert_almost_equal(self.eigvals, dmap2.eigenvalues, decimal=5)
assert_almost_equal(self.eigvects, dmap2.eigenvectors, decimal=6)
assert_raised

@raises(ValueError)
def test_wrong_weights(self):
@@ -70,4 +69,3 @@ def test_constant_epsilon(self):
epsilon=4.62827648)
dmap3.run()
assert_almost_equal(self.eigvals, dmap3.eigenvalues, decimal=5)
assert_almost_equal(self.eigvects, dmap3.eigenvectors, decimal=5)