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Diffusion Map Refactor/Implementation #863
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c511ead
new analysis feature: diffusion map
3be892e
description of diffusion map
3ce705a
diffusionmap minor fix
328c27a
test for diffusionmap
d2d4593
diffusionmap faster test
ed5f4c5
included notes
2947c0f
initial work for refactor
jdetle 7e94a58
functional refactor
jdetle ab7f93c
updated changes
jdetle 43144e0
iteration error
jdetle 18c84ee
refactor of @euhruska diffusion map
jdetle 0da96fa
removed deco import
jdetle 2c93f2d
added tests, fixed logger issue
jdetle 49578a0
style fixes, protection fixes, added docs
jdetle 7ec486a
fix of some broken areas
jdetle f350eaa
small docs fix
jdetle 245d2e8
Constant epsilon tests
jdetle 17fced2
updated CHANGELOG
jdetle 14b08e4
fixed selections and updated tests accordingly
jdetle cfcbfe0
switched order of imports [skip ci]
jdetle 07a83d1
Separated calculation of distance matrix from diffusion
jdetle 6faec56
Working refactor
jdetle 48c27a9
Change of direction in API, more work to be done implementing everything
jdetle fe08866
added timescaling, fixed some parts
jdetle cafeb68
Automodule added, Changed some object oriented stuff around
jdetle bb394ec
Changed things around to get embedding working
jdetle 074a950
Docs fixes
jdetle 68f2928
Added tests, found bugs, squashed bugs.
jdetle 98e899b
Eliminated square of distance, random mistake
jdetle b893244
Now witness the firepower of this fully armed and
jdetle 7b12ece
Satisfying the linter
jdetle e5a3487
Updated docs
jdetle cbf685d
Fixed bug in _single_frame()
jdetle e0ed7b4
Eliminated spectral gap function... for now
jdetle 303b816
Fixed matrix multiplication bug
jdetle 01dc0d5
Better single_frame loop
jdetle 2f2db09
Refactor of code to stop DiffusionMap inheriting from AnalysisBase
jdetle 34b1e7c
Removed epsilon class from pull request, now must supply a constant a…
jdetle 7c56863
Added exception to be thrown for large distance matrices.
jdetle bd40f38
Updated diffusion map after some test-driven development, added error…
jdetle 420edd0
Fixed some docs [skip ci]
jdetle c058c6c
Change to warning
jdetle b6c309a
Updated CHANGELOG
jdetle 8ba1a58
Fixes as suggested to be more pythonic and elegant
jdetle aa22772
Fixes to docs, Transform function.
jdetle 97c3105
Removed anisotropic kernel creation. Figured out that I was
jdetle b3b2ce9
Small style change
jdetle c5d1958
Updated docs to remove references to anisotropy, update tutorial [ski…
jdetle d7cd454
Added link to jupyter notebook [skip ci]
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updated CHANGELOG
commit 17fced2171914d8e5870323c9f89e26164e59da5
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why does @jandom stand in the authors now?
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I have absolutely no idea 😓