New Method visualize.contacts and extensive testing #47

gph82 · 2018-05-22T14:00:25Z

No description provided.

…achtelung, regspace_from_distance_matrix

…in save_traj

…rg in get_repr_atom_for_residue()

…handles "_CtcsInWid"; ClickOnAxisListener handles ContactInNGLWidgets, recomputes kdtree on zooming

…and listyfies

… and slice(idxs) for lists

…ish with so few frames

…dxs==[]

…achtelung, regspace_from_distance_matrix

…in save_traj

marscher · 2018-05-23T23:14:49Z

now we have "random" hangs at the notebook tests...

gph82 · 2018-05-24T10:50:18Z

yes this is the interval_schachtelung, I suspect. I'll factor in some condition to exit when the schachtelung gets trapped

…e loops

codecov-io · 2018-05-25T08:56:22Z

Codecov Report

Merging #47 into master will increase coverage by 0.12%.
The diff coverage is 94.14%.

@@            Coverage Diff             @@
##           master      #47      +/-   ##
==========================================
+ Coverage    96.1%   96.22%   +0.12%     
==========================================
  Files          13       13              
  Lines        2129     2491     +362     
==========================================
+ Hits         2046     2397     +351     
- Misses         83       94      +11

Impacted Files	Coverage Δ
molpx/generate.py	`100% <100%> (ø)`	⬆️
molpx/tests/test_visualize.py	`99.46% <100%> (+0.06%)`	⬆️
molpx/tests/test_bmutils.py	`99.82% <100%> (+1.6%)`	⬆️
molpx/_bmutils.py	`99.58% <100%> (+3.57%)`	⬆️
molpx/tests/test_linkutils.py	`87.02% <73.59%> (-11.22%)`	⬇️
molpx/tests/test_generate.py	`96% <96%> (ø)`
molpx/visualize.py	`99.4% <97.36%> (+0.05%)`	⬆️
molpx/_linkutils.py	`97.98% <98.43%> (+0.11%)`	⬆️
... and 1 more

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gph82 · 2018-05-25T09:36:24Z

The tests do get hang up (e.g. here for 15 min https://travis-ci.org/markovmodel/molPX/jobs/383598850#L970) but that line runs quickly on other tests and locally in my machine. I'd merge this for now (new features are coming) and see if we get more info on the way to the next release (soon)

marscher · 2018-05-25T10:08:09Z

Develop new stuff without functional CI will cause headaches later on (just my honest opinion).

gph82 · 2018-05-25T10:09:50Z

So how do we find out where/why it is hanging?

marscher · 2018-05-25T10:10:35Z

execute with --boxed and --timeout=120 (the latter would require pytest-timeout or so)

gph82 · 2018-05-25T10:12:33Z

you suggest we do that locally first, right?

marscher · 2018-05-25T10:13:09Z

On 05/25/2018 12:12 PM, Guillermo Pérez-Hernández wrote: you suggest we do that locally first, right?

I thought the test are only hanging remotely?

gph82 · 2018-05-25T10:14:26Z

At some weird, irreproducible moments, they also hang locally

…) and MSM() refactor and documented

gph82 and others added 30 commits May 3, 2018 11:58

[visualize] bugfix

320e36f

[bmtuils] new methods regspace_cluster_to_target_kmeans, interval_sch…

c06c791

…achtelung, regspace_from_distance_matrix

[generate] adapt to new method regspace_cluster_to_target_kmeans

973d938

[generate.projection_paths] think about not returning the data

f805b1e

[_bmutils] New class corr_dict, uniform kmeans init, avoid geom.join …

5275d79

…in save_traj

changes for the paper figures, to be reverted later

5d0f1e7

[bmutils] new method get_repr_atom_for_residue

f61759c

[visualize] fix hacky color handling

4f7dca0

[_bmutils] new method atom_idxs_from_general_input

c0dc480

[visualize] prepering traj() to allow for input feature

69acc71

[visualize] new method contacts() and optarg verbose for FES()

f308e37

[_bmutils] refactor interval_schachtelung() and elimiante unused opta…

d16a90c

…rg in get_repr_atom_for_residue()

[_linkutils] new class ContactInNGLWidget; link_ax_w_pos_2_nglwidget …

f5da7b8

…handles "_CtcsInWid"; ClickOnAxisListener handles ContactInNGLWidgets, recomputes kdtree on zooming

[_bmutils] regspace_cluster_to_target_kmeans catches non-list inputs …

c1ac4e8

…and listyfies

[visualize] feature() accepts only MDFeaturizer (corrected docstring)…

248ae82

… and slice(idxs) for lists

[test_molPX] reduced nr input features s.t. TICA does not return rubb…

99f2617

…ish with so few frames

[test_bmutils] refactor to regspace_cluster_to_target_kmeans

f0b2825

[test_visualize] update to visualize.feature() taking only MDFeaturizer

6e7bfe1

[_bmutils] get_index_ascending_coord check for len(idxs) instead of i…

f8f329f

…dxs==[]

[test_visualize] minor refactor

030930e

[test_bmutils] increase use the TestWithBPTIData class, add new tests

19615ab

[visualize] bugfix

10f6e94

[bmtuils] new methods regspace_cluster_to_target_kmeans, interval_sch…

4c934b4

…achtelung, regspace_from_distance_matrix

[generate] adapt to new method regspace_cluster_to_target_kmeans

f7421fb

[generate.projection_paths] think about not returning the data

6c2f99a

[_bmutils] New class corr_dict, uniform kmeans init, avoid geom.join …

7343dfa

…in save_traj

changes for the paper figures, to be reverted later

a2b2b7f

[bmutils] new method get_repr_atom_for_residue

4bcc967

[visualize] fix hacky color handling

608339c

[_bmutils] new method atom_idxs_from_general_input

f9d4198

gph82 and others added 6 commits May 23, 2018 16:44

[_linkutils] ContactInNGLWidget refactor

b4b681b

[tests] increase coverage

c6a233e

Merge branch 'master' into allow_input_feats

2cfebfc

[meta.yml] add nose to the reqs

432f3ad

[test_visualize] remove the evil Agg backend

197e09b

agg f

6e78d0c

gph82 added 2 commits May 25, 2018 10:55

[_bmutills] interval_schachtelung new optarg maxiter to avoid infinit…

f27c596

…e loops

[tests] remove useless import

ff3aaf5

gph82 and others added 5 commits May 25, 2018 12:28

[docs] documented visualize.contacts()

1e16f06

[tests] added the duration flag

3855e37

[notebooks] updated and included visualize.MSM method

bb01921

[visualize] new method MSM

0864fc5

[visualize] MSM minor bugifx

af6a9d8

gph82 force-pushed the allow_input_feats branch from 6601f1b to af6a9d8 Compare May 28, 2018 16:26

gph82 added 6 commits May 30, 2018 16:04

[_linkutils] minor in docstring

fa8d2ed

[visualize] sample() makes a copy of input (otherwise it gets altered…

876e5cc

…) and MSM() refactor and documented

[docs] updated

df93fbc

[tests] visualize.MSM() extensively tested

843f827

[notebooks] updated

56ba6b9

[notebooks] opsin data

7f30a3a

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New Method visualize.contacts and extensive testing #47

New Method visualize.contacts and extensive testing #47

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New Method visualize.contacts and extensive testing #47

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New Method visualize.contacts and extensive testing #47

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