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Vamp crossvalidation #1093
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Vamp crossvalidation #1093
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@@ Coverage Diff @@
## devel #1093 +/- ##
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+ Coverage 90.48% 90.52% +0.03%
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Files 188 189 +1
Lines 19016 19198 +182
==========================================
+ Hits 17207 17379 +172
- Misses 1809 1819 +10
Continue to review full report at Codecov.
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I will. I'm still working on a convenience function.
Am 18/05/17 um 22:28 schrieb Martin K. Scherer:
…
@franknoe <https://github.com/franknoe> You wanted to include this for
the next release, right?
please ping me, if when this is ready to go.
------------------------------------------------------------------------
You can view, comment on, or merge this pull request online at:
#1093
Commit Summary
* Implemented VAMP scores and crossvalidation for MSMs
* fixed variational metric problems
* Added tests for score function
* Merge branch 'vamp_crossvalidation' of
https://github.com/markovmodel/pyemma into vamp_crossvalidation
* Tested variational score
* Merge branch 'vamp_crossvalidation' of
https://github.com/markovmodel/pyemma into vamp_crossvalidation
File Changes
* *M* pyemma/_ext/variational/__init__.py
<https://github.com/markovmodel/PyEMMA/pull/1093/files#diff-0> (3)
* *M* pyemma/_ext/variational/solvers/direct.py
<https://github.com/markovmodel/PyEMMA/pull/1093/files#diff-1> (168)
* *M* pyemma/msm/api.py
<https://github.com/markovmodel/PyEMMA/pull/1093/files#diff-2> (38)
* *M* pyemma/msm/estimators/_dtraj_stats.py
<https://github.com/markovmodel/PyEMMA/pull/1093/files#diff-3> (4)
* *M* pyemma/msm/estimators/maximum_likelihood_msm.py
<https://github.com/markovmodel/PyEMMA/pull/1093/files#diff-4> (243)
* *M* pyemma/msm/models/msm.py
<https://github.com/markovmodel/PyEMMA/pull/1093/files#diff-5> (2)
* *M* pyemma/msm/tests/test_msm.py
<https://github.com/markovmodel/PyEMMA/pull/1093/files#diff-6> (23)
* *M* pyemma/util/linalg.py
<https://github.com/markovmodel/PyEMMA/pull/1093/files#diff-7> (4)
* *A* pyemma/util/metrics.py
<https://github.com/markovmodel/PyEMMA/pull/1093/files#diff-8> (231)
Patch Links:
* https://github.com/markovmodel/PyEMMA/pull/1093.patch
* https://github.com/markovmodel/PyEMMA/pull/1093.diff
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--
----------------------------------------------
Prof. Dr. Frank Noe
Head of Computational Molecular Biology group
Freie Universitaet Berlin
Phone: (+49) (0)30 838 75354
Web: research.franknoe.de
Mail: Arnimallee 6, 14195 Berlin, Germany
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Alright, this is ready. When tests are passing, this PR can be merged. |
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Alright, thanks a lot. |
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hold on, I am just testing a case that wasn't covered. |
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Do you mind adding also a changelog entry in doc/source/CHANGELOG.rst? You can skip the tests by adding a [ci skip] to your commit message, then. |
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Sure, will do that. |
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Actually we'll go for 2.4, as this is a new feature. |
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On 05/18/2017 07:36 PM, Frank Noe wrote:
Actually we'll go for 2.4, as this is a new feature.
Does it break the API? Because this would be indicated by this version number.
|
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No, but we also have new version numbers for significant new features.
It's definitely not just a patch or service release.
Am 19/05/17 um 02:37 schrieb Martin K. Scherer:
… On 05/18/2017 07:36 PM, Frank Noe wrote:
> Actually we'll go for 2.4, as this is a new feature.
Does it break the API? Because this would be indicated by this version
number.
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--
----------------------------------------------
Prof. Dr. Frank Noe
Head of Computational Molecular Biology group
Freie Universitaet Berlin
Phone: (+49) (0)30 838 75354
Web: research.franknoe.de
Mail: Arnimallee 6, 14195 Berlin, Germany
----------------------------------------------
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On 05/18/2017 07:39 PM, Frank Noe wrote:
No, but we also have new version numbers for significant new features.
It's definitely not just a patch or service release.
OK, just feel free to change it in the changelog.
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Changelog is up to date. @fnueske , I have also implemented the variational score for OOM-reweighted MSMs. I have the impression that it's not super-stable. Also, cross-validation is currently inefficient - I think we should divide the count matrix instead of splitting trajectories, but we need rewrite a few things in the estimator to allow that. Let's discuss it at some point soon. |
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The failure is due to a random event in the Bayesian estimator test. We should really remove those at some point. Going to merge. |
marscher
added a commit
to marscher/PyEMMA
that referenced
this pull request
Sep 1, 2017
commit 536211ab4c99c25720bcc16932831ceed4408044
Merge: 5b0bbbb9 9d5188bf
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri Aug 25 19:28:35 2017 +0200
Merge pull request #1149 from marscher/fix_pybind11_include
Fix pybind11 include
commit 9d5188bfd1ba0c76b9856d35baa588e2d2861e6d
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 24 17:56:30 2017 +0200
[setup] remove the non-sense pybind11 python package.
commit 954078066ca223f0598eb74b3e84d7fb44dd1d41
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 24 17:53:24 2017 +0200
[setup] if source base is a git clone, initialize sub-modules.
commit ae335b4fb24e3af07d970d1d4605e29b5be5ad82
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 24 17:43:08 2017 +0200
[setup_util] fix detection of openmp
commit a90a31acc62dbeca2a2ed6475b486c01cfbf3b7c
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 24 17:42:52 2017 +0200
[setup] use submodule headers of pybind11
commit e2c7925054611b9efdd58ecb4dd7e70c79855dbe
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 24 17:42:33 2017 +0200
[manifest] include pybind11 headers
commit 8c6e344839afb6f41914419a1355c1fbb19e17f4
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 24 17:26:27 2017 +0200
added pybind11 as submodule (v2.1.1)
commit 5b0bbbb91b18aa0f4d0945dd67e23f8775ca7fdb
Merge: 887420aa 0b806cd9
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Wed Aug 23 14:03:46 2017 +0200
Merge pull request #1147 from marscher/covartools_cpp
Covartools cpp
commit 0b806cd9f2f7177e8e13f20794660f6b600e5083
Author: marscher <m.scherer@fu-berlin.de>
Date: Wed Aug 23 14:02:30 2017 +0200
[doc] amend changelog [ci skip]
commit 7d401a018bc6226f5ed803bf38d2cfe6dd924bd6
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Aug 22 22:24:55 2017 +0200
cmp
commit d06dd67e9edbe36fd5accc50f27ed186740396f3
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Aug 22 22:19:21 2017 +0200
remove redundant parameters, lazy import (avoid loading extension, if not needed)
commit 44ffbf3a6ceb4ecdfdb8ef1954351f0357eed799
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 22 21:56:55 2017 +0200
fix compilation
commit 58cc560eb25958c8149c560bb89778fdc7735b2f
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 22 20:27:58 2017 +0200
pass tolerance as float instead of dtype
commit df341a2dcec50501ef61c2cb0155e3326556a0ce
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 22 20:11:35 2017 +0200
build covartools
commit 8175e3c9ee9b93e323feed40f368ec3b786e7510
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 22 19:55:27 2017 +0200
use template code branch elimination.
commit bd62b70304fc84b8acabb1b4032932b53437fcd3
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 22 19:46:10 2017 +0200
simplified
commit c36327dc8e79dceaa8baba36c084437f441d4d49
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 22 18:58:02 2017 +0200
replaced cimpl substract_row with numpy.substract.
commit 31cb541653d6a575d3c92493572d5e1b0c3796b8
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 22 18:16:54 2017 +0200
[covartools] use pybind binding
fixed some bugs
commit 887420aae35161bf3d26f0198eb4037bc46b298b
Merge: e1bcdd94 3cbd69c9
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri Aug 18 15:08:23 2017 +0200
Merge pull request #1146 from marscher/revert_dtrajs_removal
Revert dtrajs removal
commit 3cbd69c918f610de0c648618dd46cbf5821f80c1
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri Aug 18 13:55:57 2017 +0200
[msm] revert follow up
commit 206599e4259df90d920924784926d248d70fd148
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri Aug 18 13:04:55 2017 +0200
Revert "Merge pull request #1082 from marscher/msm_remove_dtrajs_attr"
This reverts commit 16dd0c3527322850e58dc185999233ddc32fb58f, reversing
changes made to 86b48a8acf8dc6deadb919255e268791cfebb057.
commit e1bcdd94684e92d0e3977c58338e628f1531de87
Merge: b2fb4e4a 80a8c0f0
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri Aug 18 12:13:27 2017 +0200
Merge pull request #1145 from markovmodel/revert-1134-follow_up_deprecate_dtrajs_storage
Revert "[msm] follow up on dtrajs storage removal in MSM estimators"
commit b2fb4e4a89b1d9ebacb8246468deca03ca59a1d9
Merge: f5d4b450 3d77c365
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri Aug 18 04:35:45 2017 +0200
Merge pull request #1106 from marscher/msm_mincount_connectivity
[msm] added mincount connectivity
commit 80a8c0f0247b36c7a06cfd71c65d2b0a34702ab9
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri Aug 18 03:08:46 2017 +0200
Revert "[msm] follow up on dtrajs storage removal in MSM estimators"
commit 3d77c365292e489feedfc427da4cdae66528f116
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri Aug 18 03:07:30 2017 +0200
test: removed randomness to ensure we get a connected set
commit f5d4b4501a079eeaae912df3ea07fb424bb7589e
Merge: 1a6fc6b7 aedfcbc4
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri Aug 18 01:59:52 2017 +0200
Merge pull request #1143 from marscher/h5_reader
HDF5 reader
commit 97e853d5b12a59a93b7c2fff5cd86216492041f2
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri Aug 18 01:53:03 2017 +0200
[appveyor] use np-1.12
commit 1a6fc6b7ecc26f36e5d5a5691321a25531767e5a
Merge: 18cd8c86 e38c62d4
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri Aug 18 00:59:33 2017 +0200
Merge pull request #1144 from marscher/fix_868
fixes #886
commit aedfcbc44537a4b222923e7c5924962c439529eb
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu Aug 17 23:57:28 2017 +0200
[recipe] white-list omp num threads
commit e38c62d43d983c5427198c683e2998c330083d06
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 22:29:53 2017 +0200
fixes #886
commit 18cd8c866f0aa8bc859ec007c97ffb49470439f1
Merge: aeb92e13 8c58580d
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu Aug 17 22:00:25 2017 +0200
Merge pull request #1142 from marscher/clustering_cpp
[Clustering] Modernized C code to C++ (pybind11 binding)
commit 8c58580d1aceb30dc30109c36de86bf0d68ca602
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 20:21:04 2017 +0200
[recipe] install gcc also on osx
commit 5c83ce67f95f58c05868dd4848c5f79dfbc98a09
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 19:09:37 2017 +0200
f
commit 0e85095057c2ab2266e7b6eb2dc8349aa49cb2aa
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 18:24:03 2017 +0200
[njobs_mixin] only one assign
commit 5b00ff08539f69a95d627a3109bf7d7d00a246d8
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 18:22:23 2017 +0200
cleanup
commit 63017b17101cbb2adbe97207609e7e83eec81d64
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 18:16:41 2017 +0200
[recipe] white-list OMP_NUM_THREADS
commit 6b5f386733ea0131d86501c8027bfafa010d7762
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 18:16:19 2017 +0200
[travis] added numpy-1.13 to matrix
commit 74163f4e3e1bac9445871c7aa7235457b822f8a0
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 18:01:21 2017 +0200
cxx11
commit b7c903bbf70592db357bd099a7dfcf43a6dbdf28
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 17:41:04 2017 +0200
[travis] fix pinning
commit c50b9ef129b67572d712b8e22552a5f79cfa7753
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 17:20:12 2017 +0200
added threading_util.h
commit 47542d729237fe8c3a11c4f7d46d4aeba49f068a
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 17:19:22 2017 +0200
minor [ci skip]
commit 969669791634051355b097e5383eb75adb622735
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 17:15:22 2017 +0200
release build flags
commit 574b9fe1455803b6f061ba17b739709299c763bf
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 17:11:50 2017 +0200
added tests
commit b91158221d3691c4df84dc5dbeb2708e9613aa47
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 17:11:35 2017 +0200
use double precision for potentials
commit 50e7ddb57800a6fabebbc90d7d3e457720c46dc3
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 15:33:45 2017 +0200
const
commit bc93a64117bc89c20b993e3ed452c25f14e5b2ef
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 17 15:31:43 2017 +0200
dtype
commit 7980ec1f43d1bdb3719f34d0e41a676acfc858e7
Author: marscher <m.scherer@fu-berlin.de>
Date: Wed Aug 16 13:54:23 2017 +0200
[travis] pin only major version of conda-build
commit c4662fbd94f1188d34eddc1b6f40bf7966d726b1
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Aug 15 13:14:53 2017 +0200
renamed chunksize arg to chunk_size; try mdtraj.h5 first prior new
reader
commit 5c59da3fde25294e0e2928634ebe4c72c100b3ac
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 19:12:14 2017 +0200
added source binding. Our reader takes precedence over mdtrajs custom traj format.
commit ee2186411e6f921684a4cf66cc57fd799855b349
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 18:51:46 2017 +0200
revert dbg [ci skip]
commit 9012c814c3acf6fbbdbfcd37d766a971df89fe51
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 18:27:47 2017 +0200
clean
commit 0c1eb4648b552575723885baded163d728e97216
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 18:22:18 2017 +0200
[recipe] added h5py
commit 27a895e5ba68d98d7be18541a41673f5f105180e
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 18:15:48 2017 +0200
[coordinates/readers] Added reader for HDF5 format
Because a HDF5 file can contain multiple distinct data sets,
we provide a selection functionality with regular expression
support. All the matching data sets (their absolute path) will be
considered as unique trajectories.
At the moment the selection can only be a single string, but we
should add a mapping for {filenames: selection} in the future
in order to be more flexible.
commit 5828d9b32077a5d3929697a4d982ae8719cb01fd
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 14:44:06 2017 +0200
[interface] removed wrong alias to clustercenters
commit e3614ec0e035fbd406b1a85413df07ba8001baad
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 14:41:00 2017 +0200
[kmeans_impl] fixed a bug in kmeans++ (loop was always terminated)
* n_threads == 0 will force usage of serial code.
* added, but untested std::thread impl for parallel cluster.
* use std::size_t everywhere.
* use omp parallel for reduction where applicable.
* code style.
commit 0c3a829dba6cef8800c7175ea1fce78f26b2972e
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 14:19:58 2017 +0200
dbg compile flags
commit a0f6deaa1c45e29d6efea9dc14e865775c3355c8
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 14:19:47 2017 +0200
kmeans save initial centers (dbg)
commit 9023806a1dd7097c71aadf77d95020c6fe2c618c
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 14 14:18:08 2017 +0200
added tests, changed fixed_seed test to test serial vs. parallel
commit 77eaf0ca78cc9449a2d176e57fd40e3f8d1fd6cd
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Aug 11 14:33:10 2017 +0200
clean
commit 34094c30cf1ee1f0830c82de554d7390f8e4f271
Author: marscher <m.scherer@fu-berlin.de>
Date: Wed Aug 9 16:48:42 2017 +0200
fix test
commit 888a81c3e6fefd7b697c589eedcca36f30980b40
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 7 16:32:38 2017 +0200
fixed kmeans clustering; added pre_centering for minrmsd
commit f8e33a9ca889591989a66d5c80ac54a72df23cc9
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Aug 7 11:26:33 2017 +0200
clean
commit 4282a6488234e0d2910a1a6e6d8dcbf6fb8c3c9c
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Sun Aug 6 13:31:45 2017 +0200
change assertion into exception.
commit 3c63d64ae0a844aee1c45f931375b50498633ebc
Merge: fa81ff65 e6a74ec6
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Sat Aug 5 15:34:36 2017 +0200
Merge branch 'clustering_cpp' of github.com:marscher/PyEMMA into clustering_cpp
commit e6a74ec6b6330484bfff09c0b6d79bbff06994ac
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Aug 4 20:09:01 2017 +0200
pass callback func only if show_progress is enabled.
commit 89a70291a3ea5823528e7ca235302aa2f0e495da
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Aug 4 20:00:46 2017 +0200
set n_threads in assign.
commit ade70e276f4f50e9dca7508b650726d366aa853e
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Aug 4 19:59:34 2017 +0200
more sections parallel.
commit c3b751fda716006bcfeb64c5b58912ea755be5ef
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Aug 4 19:29:32 2017 +0200
openmp for cluster, same pattern as in assign.
commit 0a3ac78ce65d78d50a5d0268b3a29ac6c481a535
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Aug 4 18:14:04 2017 +0200
dbg
commit cf2016680e164ec3fceddcf25024cd828a915956
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Aug 4 15:21:32 2017 +0200
omp cluster
commit 7aca7a68b77c8ed67d3a376680b3b5ee78122d33
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Aug 4 14:12:10 2017 +0200
Revert "remove cmake lists"
This reverts commit 731aa57c4fc6dbbe429fa6dcbe5b2240d0a91a55.
commit fa81ff65ac3bafce9a88d454ad537b47a7a2989c
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri Aug 4 09:10:56 2017 +0200
Revert "remove cmake lists"
This reverts commit 731aa57c4fc6dbbe429fa6dcbe5b2240d0a91a55.
commit 5a9a058195046318885820bde9f9a1b6dc565220
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 3 18:30:54 2017 +0200
added test
commit 25fc8adec79a84516873db5739cd82f2e8c3e8db
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 3 18:26:00 2017 +0200
implemented resume iteration for kmeans and minibatch kmeans.
Fixes #831
commit ab05a39ea84d7f1a7b6fa2fd2ca72c181c58ee3f
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 3 16:17:27 2017 +0200
remove dbg log
commit 605b18be3a85e73c4c8b36e075035533e87493a9
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 3 16:15:22 2017 +0200
fix division by zero error in convergence check
commit f0d4b4651bc5e236ee399ee23e6831a1d9f89e8e
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Aug 3 16:01:06 2017 +0200
logical keywords... msvc sucks
commit 30071a01fa9306800679779140e006364b677e81
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu Aug 3 12:40:55 2017 +0200
removed template keyword
commit 96463162089c7aff7a7c8927e39460237cb8595d
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Aug 2 19:17:18 2017 +0200
shutup m$vc
commit 3abaddb0ed10fc047727ccef6888d3c16fc48cb1
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Aug 2 19:14:19 2017 +0200
depend on gcc on linux
commit 731aa57c4fc6dbbe429fa6dcbe5b2240d0a91a55
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Aug 2 18:25:15 2017 +0200
remove cmake lists
[ci skip]
commit 12b9418ccfc8f5259e185e884692ef936476bd21
Merge: 1232fa3d aeb92e13
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Aug 2 18:17:08 2017 +0200
Merge remote-tracking branch 'origin/devel' into clustering_cpp
commit aeb92e131b22cc7ce42d392e8f8c44d057617162
Merge: c78eb577 b2ebcd24
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Wed Aug 2 16:51:04 2017 +0200
Merge pull request #1141 from marscher/deprecate_py27
[version-check] added user warning about py27 deprecation
commit b2ebcd245f5d5333d0039a5ab45d6fb6cbec1335
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Aug 2 16:48:25 2017 +0200
[ci] removed py27 from build matrices
[ci skip]
commit 174174ed7dc3f3737ff7ed6e49f705205d56b6c3
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Aug 2 16:42:39 2017 +0200
[version-check] added user warning about py27 deprecation
[ci skip]
commit 56454f32d5d81b885e39df4d74e5bb104d7cfc90
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Aug 2 15:52:24 2017 +0200
merged devel
commit 1232fa3d64d0de5d52f95a066d2ccfc0e6b2ae80
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Aug 2 15:45:48 2017 +0200
[ci] removed py 2.7 from Appveyors build matrix
commit 105408a8c6129573358baef6ca51423e1fe3f9a2
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 20:44:00 2017 +0200
remove gcc dep
commit 924db5d6b5d30d6a2d878b0f247bb530c29725c1
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 20:33:54 2017 +0200
fix compilation cxx11
commit 7e4edc2720b13cc291fd0c8a2f1e5b45a001a7c1
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 20:25:20 2017 +0200
back to cxx14
commit ae227c9226664c4a5fef804d20cdd4847a782a16
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 20:24:56 2017 +0200
use conda-forge gcc
commit 3bb3f0d09217ca8224818caaa88d8c71f4680a03
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 20:12:09 2017 +0200
use cxx11
commit 3239e8a477e5171b874bd435ae03e6f60604dc27
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 20:01:42 2017 +0200
fix pkg name
commit 50d0b3e28d0d2ba5c7262668917d80cd916ed838
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 19:56:17 2017 +0200
added changelog entry
commit 4ada1b620c019d2886b065a4aaa81a4989a444ed
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 19:55:42 2017 +0200
removed pybind f
commit 592775eff390d446bc011e22ce97719f983e61c6
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 19:54:44 2017 +0200
removed pybind submod
commit befd362a3f80355e753c9d94a80b835e903cc543
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 18:01:19 2017 +0200
added pybind to meta.yaml
commit 98eeaddb042ead4cf7a0198f19e9e90554d0e40b
Merge: 3a68a956 2957ff61
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 17:54:05 2017 +0200
Merge branch 'kmeans_cpp_try_np_array_returns' into clustering_cpp
commit 2957ff6125693112cd1e468b921bed07743f4ee4
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 17:32:39 2017 +0200
added some sanity checks
commit ef7a52eccb5a705b0474a6ed1149600d7eb9b1ad
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 17:31:55 2017 +0200
fix kmeans++
commit 5cf06ef5ec5a70d2796f3a07cdd1e2cb7932ff66
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 17:30:41 2017 +0200
fix uniform init_strat
commit 3a68a956e1d844ae35d64405d3720d6995814f9f
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 14:08:54 2017 +0200
fix length in memcpy kmeans++
commit 43ade26bed376ed9904fcd165536db067f288fa6
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Aug 1 13:59:59 2017 +0200
return a numpy array instead of copying around buffers.
commit 12a53e239d241b69d076efacad8a6569a0e89dbd
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 28 12:04:52 2017 +0200
const
commit ede4f4f51ad2d6436bd434f900875f147edffb78
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 19:06:20 2017 +0200
minor
commit ea19da85ec82f9a85ec214577795702a5ff58fa7
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 19:05:41 2017 +0200
[kmeans++] use raii for buffers, use cxx11 random number generator.
commit 0ae9179d4e3796a2bf760147d3c78fb0c6c01fab
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 18:11:48 2017 +0200
fixes
commit 580393179c182c40853cabe51e81c3f1b0df1fe3
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 17:21:37 2017 +0200
f
commit c7a4dd82129900ff46b2ffdf0574432b49d497ed
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 17:21:13 2017 +0200
del obsolete files
commit bffee36350517d060021d98c0f6bf58f39626919
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 16:51:31 2017 +0200
[kmeans] fix #1139
commit dc0fad8dbcbdc5daf7a44aa68369759979ab8922
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 16:37:41 2017 +0200
added assign method to kmeans c interface
commit 1a3e6969cc3dac8c1325ce86c750aa38e701f67f
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 16:30:09 2017 +0200
moved clustering tests to clustering.tests package
commit 6f460d8dc9115b33e1272eae2d8e42b8fedd30cf
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 16:29:26 2017 +0200
[opt] reuse clustering extension instance.
commit 420924ceccebb648b833620f93838b26946ac277
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 15:43:35 2017 +0200
formatting
commit 104d89c353c759bf33ddd2a68ae1a292efbf31a4
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 25 15:43:23 2017 +0200
f
commit 1d165216cd78f54f21a9ac3d979ba97cee137064
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jul 24 20:23:20 2017 +0200
wip
commit 5ee5386db57be14272a55c07ce96147cff245fd0
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jul 24 20:19:06 2017 +0200
kmeans works (TODO fix seed)
commit 734861981110eb018e3846fb2b96f7cb507a5787
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jul 24 17:28:15 2017 +0200
moved kmeans impl to bis, unified module
commit 050d0f7a37c0d60691ef40f750cd7a8290cafc07
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jul 24 15:58:36 2017 +0200
fix assignment
commit d5e8a949bcfc0c2ad1f071747acce627a4fb5def
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 21:00:52 2017 +0200
added todo
commit 051e7c246ccd683eb831a801284c7c4f777bafc8
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 20:39:18 2017 +0200
wip
commit 1ed933f64d517b28ad8cfadfb8c664d77b1d6b77
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 20:32:01 2017 +0200
metric assign
commit 4fa59e51e364a0048236c1cc371a58d6528d4c44
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 20:29:03 2017 +0200
removed obsolete
commit a33a44bac0b0ad44f53ce11c077454489e2ce1e3
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 18:18:14 2017 +0200
fix missing call to center + clean up
commit 4915a331395ac3abf356f310f5a825752f465be9
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 18:12:46 2017 +0200
moved impl to bits
commit d027ba8edbc90bb7b2c3d936b1990868fceb9078
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 15:46:13 2017 +0200
fix shape
commit 05187631c865ac30ff3d501e3cdd0ae68874a34a
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 15:04:48 2017 +0200
fixes
commit 637287574ce59dc7c5b04eedeb76975c25457283
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 14:37:02 2017 +0200
py interface switched to new c++ code
commit fcc0fc8f34fc941e6d8324dcbe6c195423091234
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 21 14:36:35 2017 +0200
add base
commit a5468dd6324b84245ed1d1828ef1f44d1c858c2e
Author: marscher <m.scherer@fu-berlin.de>
Date: Thu Jul 20 17:24:00 2017 +0200
fix compilation. Big thanks to @clonker!!!!!elevenoneone111
commit c78eb5775817d3aea4412fa7988bf386c2bacad6
Merge: 87255628 4c7976fe
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu Jul 20 14:53:42 2017 +0200
Merge pull request #1136 from marscher/fix_hmsm_msm_init_param_clone
Fix hmsm msm init param clone
commit 4c7976fe5268c40b3cb9a437a817ab30db4b5c21
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Jul 18 13:39:17 2017 +0200
[sklearn] return prior constructing new object
commit 2abfcad7d66bacfc0c552bbabb7966a9919daf93
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Jul 18 13:30:13 2017 +0200
[ML-MSM] added missing test for cktest.
commit 8e7eecd013591e395e4b197cfc94081a24aff391
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Jul 18 13:29:58 2017 +0200
[sklearn] if an already estimated Estimator is passed, deep copy it
This is mandatory for parameter studies, which clones estimators to
provide a "fresh" and independent blue print.
Eg. there was a bug in HMM.cktest(), which does a parameter study over a
series of lag times and cloning led to forgetting derived attributes
like the count matrix of the initial model.
This is a ugly workaround for this situation and should be properly
fixed in the future, because deep copying the object multiplies the
memory footprint by every copy taken.
commit 65da9f17d776cbddeddc14efee3d3361dc7132a6
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Jul 18 13:06:57 2017 +0200
[ML-MSM] ensure passed msm_init is estimated
commit 87255628a34cc1292ff4b563c20c2dc8838502ba
Merge: 9798db07 c85f1c0b
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Tue Jul 18 02:07:29 2017 +0200
Merge pull request #1134 from marscher/follow_up_deprecate_dtrajs_storage
[msm] follow up on dtrajs storage removal in MSM estimators
commit 39893e893d156e71a2c177e50536bd8b85557050
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jul 17 19:16:22 2017 +0200
wip
commit 5d59e7c6dc551f3911b06a04fa5bd683ccb31609
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jul 17 14:50:01 2017 +0200
merged devel
commit fcd2dcfe5c1df78d7a265010f465ec0a4ff77580
Merge: bfc51ee1 9798db07
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Mon Jul 17 14:37:45 2017 +0200
Merge branch 'devel' into msm_mincount_connectivity
commit c85f1c0b5ae1829afe15e4516e9c12dd2ba5e547
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jul 17 14:15:08 2017 +0200
[msm] follow up on dtrajs storage removal in MSM estimators
commit 9798db07a61f95c36a876bf340026f0d307eee5f
Merge: f0b3d252 8a9d7167
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri Jul 14 17:28:20 2017 +0200
Merge pull request #1133 from marscher/fix_matplotlib_colormap_deprecation
[plots/2d] replace cmap='spectral' with 'nipy_spectral'
commit 8a9d7167fc1f0e519af5c70360bd36ed9c78ebd9
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jul 14 14:54:51 2017 +0200
[plots/2d] replace cmap='spectral' with 'nipy_spectral'
Fixes #1130
commit f0b3d252439749956aab91d2058407c7792427f4
Merge: e314f64a ba11803e
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Wed Jul 12 11:35:18 2017 +0200
Merge pull request #1131 from thempel/n_metastable
[msm] improve user-friendliness by adding n_metastable to MSM class
commit ba11803ed85f3aee6c430323b5df1191acc71d33
Author: thempel <thempel@zedat.fu-berlin.de>
Date: Tue Jul 11 17:47:33 2017 +0200
[msm] added test for MSM.n_metastable
commit a96f4f74c6059cfca9157d17febeda86e4d73932
Author: thempel <thempel@zedat.fu-berlin.de>
Date: Tue Jul 11 17:34:41 2017 +0200
[msm] removed obsolete deep copy of integer
commit f634dbda4703de81fa42a32b449ad82054b5a570
Author: thempel <thempel@zedat.fu-berlin.de>
Date: Mon Jul 10 17:36:22 2017 +0200
[msm] added n_metastable to MSM class for convenience
commit e314f64ab3195679266e761fc92669f093fc40ea
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 4 17:08:16 2017 +0200
[covartools] added missing declaration
commit 1c9bef640cb7c5a402c4a8c9d42b69fd33ae3396
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jul 4 15:38:15 2017 +0200
[MNT] fix a runtime warning due to a wrong formatting
featurization/misc.py:1: RuntimeWarning: divide by zero encountered in true_divide
# This file is part of PyEMMA.
[ci skip]
commit f244c4b3f4240eaf6bc7ef10c0fbcec083295f4b
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jul 3 14:14:18 2017 +0200
[msm] fix typo
[ci skip]
commit 9627352e5bbb959970a419a000a54e22ea084566
Merge: b3d54ac3 7eef75c9
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Sat Jul 1 12:15:55 2017 +0200
Merge pull request #1125 from marscher/fix_running_moments_cov_yy
[running_moments] fix computation of cov_YY
commit 7eef75c9382b2ead0da449fc1ef06c4789031d1e
Author: fabian-paul <fabian-paul@users.noreply.github.com>
Date: Fri Jun 30 19:53:42 2017 +0200
more side case fixes
commit 886f1c9e1aa7dbd605ab90c1ef36bc2df6414f36
Author: fabian-paul <fabian-paul@users.noreply.github.com>
Date: Fri Jun 30 19:44:22 2017 +0200
fix side cases
commit b3d54ac34f0804f731cd517350766ac63ee4ec29
Merge: 119bb82a b47567ce
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri Jun 30 17:45:24 2017 +0200
Merge pull request #1126 from marscher/doc_fix
[msm] fix minor doc formatting issues
commit b47567ce362a6020ec449888756a02dc1f7d7404
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jun 30 17:43:24 2017 +0200
[msm] fix minor doc formatting issues
[ci skip]
commit ae49fe27181cd611e2c8002e9af3c006902a2476
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jun 30 17:18:23 2017 +0200
[doc] amending changelog
[ci skip]
commit 928d7be26201b6b195a5612c0a888d72960d1504
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jun 30 17:09:14 2017 +0200
[running_moments] fix computation of cov_YY
commit 119bb82ad7d0a8f6b3096224033d9aebb29a9d6e
Merge: 16dd0c35 3950db9c
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu Jun 29 14:16:37 2017 +0200
Merge pull request #1116 from marscher/fix_dt_model
[MSM] fix dt_model in bayesian msm, added tests for other estimators
commit 3950db9ce5931de1c5d9865d8f4ef9c8245c3af2
Merge: 4ca786f8 16dd0c35
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Mon Jun 26 18:09:37 2017 +0200
Merge branch 'devel' into fix_dt_model
commit bfc51ee160e6c21e1937c1d5b12c09918755330e
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 26 14:21:18 2017 +0200
minor
commit 9dca2d91f82c82dfa7c352a4acf248dc2a59404d
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 26 14:15:09 2017 +0200
[doc] amend changelog
[ci skip]
commit 8fede3b3517fa3a7f36d4a05943fd391b53e2d39
Merge: 932ed857 16dd0c35
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu Jun 22 15:47:17 2017 +0200
Merge branch 'devel' into msm_mincount_connectivity
commit 16dd0c3527322850e58dc185999233ddc32fb58f
Merge: 86b48a8a 13792908
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu Jun 22 15:46:08 2017 +0200
Merge pull request #1082 from marscher/msm_remove_dtrajs_attr
[ML-MSM] towards removing dtrajs attribute (deprecated first)
commit 86b48a8acf8dc6deadb919255e268791cfebb057
Merge: eace49aa 6a394d6e
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu Jun 22 15:45:48 2017 +0200
Merge pull request #1122 from marscher/trajdb_failsafe
[trajdb] async fail-safe lru updates.
commit eace49aa678b11d72590edb0c71e458aa939c02f
Merge: d71ea44f d7255477
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu Jun 22 15:45:22 2017 +0200
Merge pull request #1120 from marscher/running_covar_weights_input
Running covar weights input possible as list of ndarrays
commit 1379290825b12c9201887cd03a99ea3aba28617b
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Jun 21 00:42:07 2017 +0200
fix tests
commit a4da545a32de6ebec2f5c9d8eca0f4ff607d4fd8
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Jun 20 23:34:14 2017 +0200
[conftest] simplified
commit 7a08047e85fe99f5e23dec4715d7c3625a644fe8
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Jun 21 00:22:26 2017 +0200
resolved conflicts
commit 12fa4c4492a114d103e21d6b10131612481b6afe
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed May 10 15:09:27 2017 -0500
remove param doc from property.
[ci skip]
commit d849526b42b6a811d5ec50847f36b332fef99ec9
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed May 10 15:06:55 2017 -0500
[oom-msm] fix activte_state_indexes
commit 8111394ca21e7d8b43bfb23c5db0d0c8a47cb63b
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed May 10 14:54:25 2017 -0500
[ml-msm] remove deprecation on hmm()
the argument check will handle this.
commit e61bfb548262c2195e4d5854b9963f799d9cf59b
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed May 10 14:48:35 2017 -0500
[test-msm] adopt deprecated calls.
commit 5d7562f21236938930035d6b290cd362c916fd1a
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed May 10 14:48:11 2017 -0500
[ml-msm] ensure dtrajs for methods accepting it.
Fix warning (show invocation location).
commit 3638274f0227a82894e9d7cf5c251263be605e1a
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed May 10 14:21:42 2017 -0500
[ml-msm] deprecate dtrajs_full|active.
To provide functionality which depends on dtrajs, add methods which take
dtrajs as argument (For now the argument is optional, but will print a
warning to the user to inform about the pending deprecation).
commit d725547741e622f3ac87127f8bc9b715ef51e1a9
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Jun 21 00:47:57 2017 +0200
fix
commit 6a394d6e6ed36f1ae9b030771a2793d44190192a
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Jun 21 00:05:43 2017 +0200
[doc] amending changelog
[ci skip]
commit dca397e67cb2c765e8e71dd107f82a0e143c0e84
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed Jun 21 00:03:30 2017 +0200
[CovEstimator] allow for non-float integral types, check len of w list.
commit 81db4518b05a90a92fad3a1de7da2faa03468843
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Jun 20 23:45:38 2017 +0200
[lagged_covar, api] set chunksize to an integer to fix a bug.
If chunksize is set to None, estimate is not callable after the object
is constructed.
commit f4bc923683151177caafc95d58aa51e6338049b6
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Jun 20 23:36:39 2017 +0200
[DataInMemory] added __str__, __repr__ -> describe()
commit 1c960be8a10651dabb0383971b27db40d75fea7a
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue Jun 20 23:34:14 2017 +0200
[conftest] simplified
commit 4a152d6ec00636ccd8ba20409095fa567217606b
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 19 17:08:59 2017 +0200
no output catching.
commit 026e0aeb935d81b6ea98b3ef20c00b8c2c8bcbf4
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 19 16:07:30 2017 +0200
fix race condition.
commit b71742d8dfcd4ac8df511c9c75ee58a2b2257bcb
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 19 15:47:21 2017 +0200
catch stdout/err
commit 0ec2952c74b588529f5be74f93f14f3769787c71
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 19 14:03:27 2017 +0200
[trajdb] better transaction handling
commit c5050fafc0a2c465a519fa09b385276e87d5eb04
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 19 13:50:48 2017 +0200
[tests] catch error message.
commit ddc881177dd72b131614c3b28f3c3577cc9f6da4
Author: marscher <m.scherer@fu-berlin.de>
Date: Fri Jun 16 17:03:31 2017 +0200
[trajdb] async fail-safe lru updates.
Fixes #1119
commit 54f0ddb1311528ee2ff9091541b49259fe3b2b82
Author: marscher <m.scherer@fu-berlin.de>
Date: Wed Jun 14 15:27:58 2017 +0200
f
commit 4ecb02d420486cae47253ce7fdc79579ca454a76
Author: marscher <m.scherer@fu-berlin.de>
Date: Wed Jun 14 14:56:31 2017 +0200
[running moments] revert broken div by zero check.
commit 000414dc79b4dff25c015cf17e6d774ed553b170
Author: marscher <m.scherer@fu-berlin.de>
Date: Wed Jun 14 14:54:49 2017 +0200
[tests] generate test data only once, fix div by zero error.
commit 9b9dadedcd4c499c23d6eef263f4a06a30c3519b
Author: marscher <m.scherer@fu-berlin.de>
Date: Wed Jun 14 14:54:10 2017 +0200
minor changes
commit 1cc58b5b16d1503b49175613f74c1879ace2232d
Author: marscher <m.scherer@fu-berlin.de>
Date: Wed Jun 14 14:42:53 2017 +0200
[StreamingTransfomer] moved estimated check to StreamingEstimatorTransformer
also made dimension abstract, since it must be implemented.
commit 4ca786f8c7e462b5f79264c75bdbe0d720b8cd46
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jun 13 13:53:20 2017 +0200
[appveyor] use recent conda-build
commit bc3b724a4524001180b00f58d32ed474d7649e94
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jun 13 12:26:19 2017 +0200
[running covar] fix division by zero for w=0
commit 9b9d89aa15e54a27cb15013eb2445afc1a1e5111
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jun 13 12:20:48 2017 +0200
[conda-recipe] added pytest-faultest as crash handler
commit d348b989d9ec6a162cda9ab2ea6e8a21a0f74bf9
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jun 13 12:18:44 2017 +0200
added tests
commit 07330a4d20c94449c1f4b42f9b29ee0a539990df
Author: marscher <m.scherer@fu-berlin.de>
Date: Tue Jun 13 12:17:01 2017 +0200
[running moments] fix type checking
commit 5fd4eafc99d8bfc63e54161becf7749dd5e43aa9
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 12 20:08:49 2017 +0200
[LaggedCovariance] added possibility to set weights as lists of ndarrays
Fixes #1113
commit 00d514ef46dd34dc7a8c1d37846ccec5f8118ae3
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 12 17:46:52 2017 +0200
[doc] amending changelog
commit 2484e79aee83115d02c14379149feea63a96e003
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 12 17:41:48 2017 +0200
fix test
commit 932ed857e80ad3a942a17faaf6a84898cace47ca
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 26 15:20:21 2017 -0500
do not overwrite the state we're trying to filter out by mincount_connectivity.
commit fe5370a78c609fafef3646667463743c51bd5f93
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 26 14:26:03 2017 -0500
added tests
commit cce1161f5516547b209b23ee25c7af3390eb9a30
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 25 14:21:16 2017 -0500
[dtraj_stats] fix sparse efficiency warning.
commit a5ba85033f4e33103db1d497a1c896dc0b5a07b0
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 25 12:20:01 2017 -0500
f
commit 364012b98cce11e3f724d0e6196476f42e5c9239
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 25 11:53:13 2017 -0500
[msm] added option mincount_connectivity
commit 7ea6012d21ec4915a99caa01c3cd7d0a7126990b
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 25 11:40:59 2017 -0500
[dtrajs_stats] added compute_connected_sets to handle mincount_connectivity
commit d71ea44ffc789c3928b68249e99e65862559e3aa
Merge: 561e23c9 1a78ea76
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Mon Jun 12 16:38:51 2017 +0200
Merge pull request #1100 from markovmodel/fix-progressbar-cset
[thermo] remove progress bar for 'finding connected set'
Fixes #1098
commit 088423736deba4461911669eeba2c7162ed248b0
Author: marscher <m.scherer@fu-berlin.de>
Date: Mon Jun 12 16:30:47 2017 +0200
]MSM] fix dt_model in bayesian msm, added tests for other estimators
Fixes #1114, #1083
commit 561e23c9457b07d6800198ecc4362f1f5ecae035
Merge: 8b187c7a 555e2a85
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu Jun 8 21:15:18 2017 +0200
Merge pull request #1112 from marscher/fix_transformer_in_memory
Fix transformer in memory
commit 555e2a85d214d201a71a02844eb07a92b83350fa
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue May 30 16:00:55 2017 -0500
[doc] amending changelog
[ci ckip]
commit f0b6204598977242af7fb4d52a6208d26c117aa8
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue May 30 15:58:51 2017 -0500
[transformer] removed unused imports
[ci skip]
commit 175d1740321b7d0de49c158f7d0a03888075da07
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue May 30 15:26:54 2017 -0500
[FragmentedReader] fix a bug, which hindered in_memory usage.
Since it did not use the public interface to create an iterator, the
flag in_memory was not used at all.
commit 23148db7977236fedacc77a36c48c6dc90112c1e
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue May 30 15:25:31 2017 -0500
[StreamingTransformer] fix a bug, which hindered in_memory usage.
Since it did not use the public interface to create an iterator, the
flag in_memory was not used at all.
commit 8b187c7a71acb5885b7fd90f6ee44fb8b72f0538
Merge: 5a95a0f6 974c8920
Author: Simon Olsson <simols@hotmail.com>
Date: Tue May 30 15:35:31 2017 -0500
Merge pull request #1111 from markovmodel/amm
Addition of AMM functionality.
commit 974c8920d0c3549600295c7ab88bdcad3fb83c6a
Author: Simon Olsson <simols@hotmail.com>
Date: Tue May 30 14:55:08 2017 -0500
fix something - break something else.
commit fd475bc200f2418c2f2603302e6fbd8459b936b1
Author: Simon Olsson <simols@hotmail.com>
Date: Tue May 30 14:52:18 2017 -0500
a few test fixes.
commit 79c59c4c6190617f30091754e30671420ffbdaa2
Author: Simon Olsson <simols@hotmail.com>
Date: Tue May 30 12:52:17 2017 -0500
Further clean up
commit b6b051d7b76deb75cab37993a06370331a53d84e
Author: Simon Olsson <simols@hotmail.com>
Date: Tue May 30 12:42:51 2017 -0500
Test clean up. Should address last comment of Frank.
commit 3e383a28632f17d631e45e0964edc0d66b694257
Merge: 052606bb 2a319343
Author: Simon Olsson <simols@hotmail.com>
Date: Tue May 30 11:46:17 2017 -0500
Merge branch 'amm' of https://github.com/markovmodel/PyEMMA into amm
commit 052606bbe9a33eb1e40413ab4b95a762c2f49b46
Author: Simon Olsson <simols@hotmail.com>
Date: Tue May 30 11:44:41 2017 -0500
Removed redundancy
commit 1a78ea7690346d82be9628e01e63970f20d4eb9d
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue May 30 11:34:03 2017 -0500
clear pg even in case of exception
commit 2a319343e04ee593042ce0595729c5e2484b14ee
Merge: c451c8c6 5a95a0f6
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Tue May 30 11:15:20 2017 -0500
Merge branch 'devel' into amm
commit c451c8c6488c607d28c71416cb70309d8c705837
Author: Simon Olsson <simols@hotmail.com>
Date: Tue May 30 00:21:17 2017 -0500
Addressing most issues raised by Frank.
commit de428412f3755e5904c0954d73f947a68786070f
Author: Simon Olsson <simols@hotmail.com>
Date: Mon May 29 23:05:30 2017 -0500
small additions
commit d17bd54fb0defc9cc906f9b2846f530ce188259f
Author: Simon Olsson <simols@hotmail.com>
Date: Mon May 29 22:58:46 2017 -0500
Last few bug fixes.
commit db97c45ce5bc4d60319b27fb23c26292d8144948
Author: Simon Olsson <simols@hotmail.com>
Date: Mon May 29 22:34:28 2017 -0500
WIP
commit b429fd80ef85cce9439fd0dbc5d5bbccecb54466
Author: Simon Olsson <simols@hotmail.com>
Date: Mon May 29 22:24:08 2017 -0500
a few bugfixes and more unit tests. a two are still failing.
commit e09ccaef53f59a3d92d3c262ef1a1bd0ca36579b
Author: Simon Olsson <simols@hotmail.com>
Date: Mon May 29 18:56:21 2017 -0500
added docstrings, unit-tests and refined api. some unit-tests are still missing.
commit ebb8457c90708aa2403baf124c565959dce9db96
Author: Simon Olsson <simols@hotmail.com>
Date: Mon May 29 14:20:27 2017 -0500
WIP
commit 2d94cc5007ddeb76d941bc7e8082e32a1a117144
Author: Simon Olsson <simols@hotmail.com>
Date: Mon May 29 12:11:18 2017 -0500
a few bug fixes
commit 5a95a0f639ddd8e1e41f7a037c44d9f74a587909
Merge: dad5b736 94a2be92
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Sat May 27 21:41:24 2017 -0500
Merge pull request #1104 from marscher/fix_state_labels_plot_networks
Fix state labels plot networks
commit dad5b736ebf25dea5f0ec46dd17430c3a44426d8
Merge: 9f0a0e48 0f8ccaad
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Sat May 27 09:03:31 2017 -0500
Merge pull request #1109 from marscher/fix_msm_modifying_ctor
[msm] do not modify parameters in ctor to comply with sklearn
commit 0f8ccaad234c399456d1210a4b6625c5a8ac1a72
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 26 23:39:01 2017 -0500
[msm] do not modify parameters in ctor to comply with sklearn
Fixes #1108
commit 1d97ecc72b8a26154473e0d331f59343c29728b2
Author: Simon Olsson <simols@hotmail.com>
Date: Fri May 26 20:42:51 2017 -0500
WIP
commit c18da220b776ecc21f0f594e6736d2218c68eb94
Author: Simon Olsson <simols@hotmail.com>
Date: Fri May 26 17:01:31 2017 -0500
WIP
commit b23454d48ae8912c4054e2879ad9a8b3148dbe4a
Author: Simon Olsson <simols@hotmail.com>
Date: Fri May 26 16:56:46 2017 -0500
added convienence function and made a few minor changes
commit 9f0a0e48ad3846c1f4d8eb68d21c0dad4a0facd5
Merge: 589a0bfa 9b156b74
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri May 26 16:20:59 2017 -0500
Merge pull request #1107 from marscher/switch_testing_to_conda_forge
[CI] switch to conda-forge for testing.
commit 9b156b7448e0d309cb22ff8d56ac7c28b07cf40d
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 26 15:36:16 2017 -0500
whitelist env CIRCLE_TEST_REPORTS
[ci skip]
commit cf1e0faf5c3d04fd54bceeb7fa8c51dfd8120299
Author: Simon Olsson <simols@hotmail.com>
Date: Fri May 26 15:15:59 2017 -0500
some changes
commit 244f66a6bc507ff65e25f7e461144a56934e4504
Author: Simon Olsson <simols@hotmail.com>
Date: Fri May 26 14:35:22 2017 -0500
more bug fixes
commit 603c1b036d359b97d7c1e3aff958b99194c3c48e
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 26 14:34:54 2017 -0500
removed obsolete file
commit e7532a0bd7f24ff791bbc0b4cd813c15c3a47d5c
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 26 14:34:30 2017 -0500
[circle] fix report
commit 3ac10a61be92d8bbc141d23f8083685bb2a2beea
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 26 14:34:05 2017 -0500
[tests] fix integer division
commit 8b340f0e87f05dab7e7040bf635fa4d4a7d7a808
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 26 14:32:00 2017 -0500
[travis] removed py34
commit 1b9668c826585592e17b49e645357734be600ba8
Author: Simon Olsson <simols@hotmail.com>
Date: Fri May 26 13:42:55 2017 -0500
further fixes
commit 3ccc3d39e00f3b489877308c432aff8d3606311a
Author: Simon Olsson <simols@hotmail.com>
Date: Fri May 26 11:34:09 2017 -0500
a few bug fixes
commit 706fb01eb246838d3f4fae5db558716b995fde7d
Author: Simon Olsson <simols@hotmail.com>
Date: Fri May 26 10:30:00 2017 -0500
minor clean up
commit f97aa0a8b6b9aea4dde971e46f1643a8b6c78d4b
Author: Simon Olsson <simols@hotmail.com>
Date: Thu May 25 17:34:04 2017 -0500
sausage
commit 00b57af6309e69f540d938408176f50a01c95c07
Author: Simon Olsson <simols@hotmail.com>
Date: Thu May 25 17:33:38 2017 -0500
sausage
commit 4dac6d1069d553df265f7cc7bc7e315f6828c433
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 25 16:27:53 2017 -0500
appveyor removed py34 from build matrix (not supported by cf)
commit 4b88148da719fa4ea52f68b76d2b53dbf70d50cb
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 25 14:39:24 2017 -0500
[CI] switch to conda-forge for testing.
commit 94a2be92ba2cf2c2898281ee27ac057ef14f96c3
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed May 24 16:49:49 2017 -0500
added some tests. use only pyemma functionality (removed msmtools refs).
commit 3bdd46a595cc600c8b56c045530d1901639a7b2f
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed May 24 16:49:04 2017 -0500
[plots/networks] fixed state_labels == 'auto', create fig if ax==None
plot_flux: If sets A, B contained more than one state, automatic state
labeling did not respect that.
NetworkPlot:
- Also the documentation states, that if ax is None, a new figure would
be created, but plt.gcf() was used. Now a proper new figure is created.
- Changed plain asserts to proper exception handling.
- added simple logging (debug).
commit 589a0bfab91174ae3a698f603fbc5f5d6e780a6e
Merge: b2158d8c 95591de5
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Wed May 24 15:21:21 2017 -0500
Merge pull request #1102 from marscher/fix_get_umbrella_sampling_data
[datasets/double_well_thermo] fix function for py3 and made tests dir a pkg
commit 95591de5832eb1fc2d7e78aa9293f28ddc8eb73d
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Wed May 24 15:19:18 2017 -0500
[doc] added changelog entry.
[ci skip]
commit e17fcd730dc8575aa910f8c6d7eb557df11fbaa6
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue May 23 18:35:41 2017 -0500
fix dict access
commit 5a6c15e9d8b0cac8d60f52369d7a3e09e9620f5a
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Tue May 23 16:34:33 2017 -0500
[datasets/double_well_thermo] fix function for py3 and made tests a pkg to ship
Fixes #1101
commit 892ad49a0aa8802a9c7fde20a63b8b0779f1c568
Author: Paul, Fabian (fapa) <fabian.paul@mpikg.mpg.de>
Date: Tue May 23 10:09:19 2017 +0200
[thermo] remove progress bar for 'finding connected set'
commit b2158d8cd7d20cef8cfc9dfb929f951aa83ac389
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Mon May 22 16:36:11 2017 -0500
[doc] fixed release date [ci skip]
commit eb9bb9ec17e0aa0638349f58defa2510bfaf54d1
Merge: d1c3989d 55a91da9
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri May 19 23:24:50 2017 -0500
Merge pull request #1096 from marscher/fix_exception_during_in_memory_setter
[Iterable] Do not update the `in_memory` property, if exception during mapping
commit d1c3989db17dac8ea2ad4254ba8bdb47abb94290
Merge: d70cac11 2332798b
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri May 19 20:32:06 2017 -0500
Merge pull request #1076 from markovmodel/fix-connectivity
Improved connectivity checks and documentation
commit 55a91da9473fb0d4232e071d910f797952e0d725
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 19:41:23 2017 -0500
[Iterable] set flag in worker methods to not to confuse derived methods.
commit d70cac11ac29111681bf5bc79afabc5512a6da72
Merge: 1a18472d 25861706
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri May 19 19:23:11 2017 -0500
Merge pull request #1097 from markovmodel/new_data
Added a generator for multi-ensemble data.
commit 2332798b0735b0ed7b8b3a0887480daa4383d801
Merge: a383ef5c 1a18472d
Author: Christoph Wehmeyer <cwehmeyer@users.noreply.github.com>
Date: Sat May 20 01:23:20 2017 +0200
Merge branch 'devel' into fix-connectivity
commit 25861706e516f44a1c3cf13703d1597e2d2cc46d
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Sat May 20 01:17:20 2017 +0200
[datasets] added unit tests for multi-ensemble generators
commit 77ece107aefa471ae030a4515e588bd7b9c37b2c
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Sat May 20 00:53:27 2017 +0200
[datasets] added PR number to CHANGELOG
commit db7ca2fe5d74047cef5824d4e10c8d091891a972
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 17:45:47 2017 -0500
f
commit 23c1d743ba80d4216214428bb1d5d36e47c70854
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Sat May 20 00:43:03 2017 +0200
[datasets] minor change and CHANGELOG update
commit d9e537f12191f6a3b39a7f6a5b375ff59bd4a341
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Sat May 20 00:34:35 2017 +0200
[datasets] added continuous asymmetric double well generator for multi-ensemble simulations
commit 1a18472d85ece0a8095236198ce6ab3b85c77a4c
Merge: fd2e5036 fa59f91c
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri May 19 16:52:27 2017 -0500
Merge pull request #1095 from marscher/refactor_conf
[config] Refactored module hack to a normal class/instance pattern. Fixed docs
commit 08e5a23cab684446c7fcc4a8db70d4976fc2d804
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 16:09:58 2017 -0500
fix + test
commit fd2e50369f12e6c9ea0adf1551014149fc36247f
Merge: 871ef700 fd12b22c
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri May 19 15:37:23 2017 -0500
Merge pull request #1091 from marscher/kmeans_seed_bool_and_int_supported
[kmeans] allow to pass the seed into kmeans
commit fa59f91c483a3381811a708737e2cc4aad43fd75
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 15:36:54 2017 -0500
[doc] amending changelog [ci skip]
commit 13cf345615d4704604db432e4ab4bf57516f6ff4
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 15:34:53 2017 -0500
[doc] amending changelog
[ci skip]
commit 7078f88d4b0d9d523de0fb7c212cd764fa624c93
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 15:29:57 2017 -0500
[Iterable] Do not update the `in_memory` property, if exception during mapping.
commit 5baddfb514d1c7a974413a2f9cb927fe90839c80
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 15:23:35 2017 -0500
[config] added mute option which silences progressbars and logging
Note that critical errors are still being logged, because we need a way to
inform users about serious errors.
commit 871ef70035220d675cf3b30b3d5fa2bf7b481e99
Merge: b9bae157 187e0c33
Author: Christoph Wehmeyer <cwehmeyer@users.noreply.github.com>
Date: Fri May 19 22:17:37 2017 +0200
Merge pull request #1094 from markovmodel/thermo-doc
Thermo doc
commit fd12b22cbd17f779744a3b4d0efa99615127ef43
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 12:31:10 2017 -0500
[kmeans.c] fix dtype of seed
commit d9825246b0975e3397773dfae330d202d65a0c2c
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 17:05:04 2017 -0500
fixed seed, allow for None and long (py27 on win).
commit 7946fc70d82194d9197ee2a06fb68764480b07eb
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 15:24:26 2017 -0500
fix
commit a35b139eb308f00232fbe5ebc00333ab1abffb6b
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 15:05:29 2017 -0500
minor
commit 39b1d49307fcfe65c4e1b740d66c0bed5b41ff4b
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 14:52:57 2017 -0500
test for too large seeds
commit 4ef4609b1cdc5e9f75178345175f8fdd73083390
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 14:49:25 2017 -0500
[coor/api] fix doc
[ci skip]
commit d2500a58514a206fdc5f5c7363a58cdd4bd9a52b
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 14:47:36 2017 -0500
[kmeans] check py int fits into unsigned int.
commit 659a31b3b13a3cc09e732175593f775cf41ad003
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 14:45:23 2017 -0500
[kmeans.c] unsigned int
commit e41b48b6f96ea3c95d6b0a41855a9bdcc2e19e6c
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 14:32:29 2017 -0500
[ci skip]
commit e74fc1410747ac93246cd4545efbc6ede95b94d2
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 14:24:40 2017 -0500
[kmeans] allow to pass the seed into kmeans
commit 175be91aa7e83990406b17009167d9506b1cdb80
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 12:12:54 2017 -0500
[doc] amending changelog [ci skip]
commit 9761015a96e47315ed2091d719b490c612adf9db
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 12:03:08 2017 -0500
fixes
commit d6fca7cdee99d06efbbf67974496f8a1e7d94e93
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 11:37:48 2017 -0500
[config] Refactored module hack to a normal class/instance pattern. Fixed docs
Now each property of the Config class has a documentation. Moved the examples
to doc/source/Configuration.rst (because numpydoc does not allow for extra
sections).
Removed all dirty hacks of a class instance pretending to be a module.
Fixes #1089
commit b9bae1574fccb72324a1897fd27690dc890bb2bd
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 10:56:03 2017 -0500
[doc] fixed changelog formatting
[ci skip]
commit dc97f5ee0e6582272d1e50a15be7fedd63a85450
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 10:45:51 2017 -0500
[doc] added changelog entries for 2.4, fix 2.3.2
commit d4478abd13a682fbd69f69305ed55e72c36bf8af
Merge: ade3d260 097216bf
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 19 10:15:01 2017 -0500
Merge branch 'changelog_233' into devel
commit ade3d260b575b16a3cb744c11aef94f8076c5110
Merge: 3f250e14 83211402
Author: Frank Noe <frank.noe@fu-berlin.de>
Date: Fri May 19 05:39:16 2017 +0200
Merge pull request #1093 from markovmodel/vamp_crossvalidation
Vamp crossvalidation
commit 83211402f51c3f08bd6ccd8f9ac91a07107b2a62
Author: noe <frank.noe@fu-berlin.de>
Date: Fri May 19 03:28:16 2017 +0200
Added score-crossvalidation for OOMs and modified Changelog
commit a6bdbdd6c3fd183c5c833891eb722745d314e2d7
Author: noe <frank.noe@fu-berlin.de>
Date: Fri May 19 00:58:46 2017 +0200
Completed docs
commit 097216bfd48efb9ae6699e4f0ca26d759ea7ef14
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 17:14:49 2017 -0500
[doc/changelog] added entry
[ci skip]
commit 2ed1094d8bf2a14f634856719590e2e648b1cdd6
Merge: d12b0340 3f250e14
Author: noe <frank.noe@fu-berlin.de>
Date: Fri May 19 00:13:31 2017 +0200
Merge branch 'devel' of https://github.com/markovmodel/pyemma into vamp_crossvalidation
commit d12b034079ac9798abf5f860dc2854430b5e57fe
Author: noe <frank.noe@fu-berlin.de>
Date: Fri May 19 00:13:26 2017 +0200
Added score_cv function to MSM estimator
commit 3f250e144c91e4b1c4a8eca6bed45386fa0c7969
Merge: 8e8d5474 6c9aa4d5
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu May 18 16:58:26 2017 -0500
Merge pull request #1088 from marscher/remove_parametrize_calls
Remove parametrize calls
commit 00a85711b39a15c02de5d9a0b77286d153c71f40
Merge: 0da90805 8e8d5474
Author: noe <frank.noe@fu-berlin.de>
Date: Thu May 18 23:30:17 2017 +0200
Merge branch 'devel' of https://github.com/markovmodel/pyemma into vamp_crossvalidation
commit 187e0c336bf60b502d6f9e2a73f55bc8e2d940c2
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Thu May 18 23:23:17 2017 +0200
[thermo] (d)TRAM uses its own pi-estimate when creating the MSM objects
commit 8e8d547433df510b9773800af38c5d474cc6c82b
Merge: 203482d0 214f01b5
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Thu May 18 15:25:45 2017 -0500
Merge pull request #1092 from marscher/update_install_instr
[doc] install instructions point to conda-forge instead of omnia.
commit 214f01b506a310876044311d9e999375e564ca41
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 18 15:17:37 2017 -0500
[doc] install instructions point to conda-forge instead of omnia.
[ci skip]
commit 0da90805236b76490b478e1a9ff3d44f76980f7c
Merge: 0c287b5e 8a8a31c9
Author: noe <frank.noe@fu-berlin.de>
Date: Thu May 18 06:05:27 2017 +0200
Merge branch 'vamp_crossvalidation' of https://github.com/markovmodel/pyemma into vamp_crossvalidation
commit 0c287b5ef00d1afb4f0c7b8b9209f81b95052099
Merge: d1725c67 157152a3
Author: noe <frank.noe@fu-berlin.de>
Date: Tue May 16 02:33:32 2017 +0200
Tested variational score
commit b1e6cb859e4a00ec9400b3e98258133e0c3ee11c
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Tue May 16 19:00:00 2017 +0200
[thermo] minor change
commit 543ca47d641d64a31cf3550025c055d100bb1d44
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Tue May 16 18:56:43 2017 +0200
[thermo] remove obsolete ground_state parameter/attribute in TRAM and DTRAM
commit 58aabef3fac88a4cdbfe27e1eadcafa047c1b3da
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Tue May 16 15:38:46 2017 +0200
[thermo] minor change
commit 22ea82ab21268e8652334d48d0246933fe7eb8a3
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Tue May 16 15:06:26 2017 +0200
[thermo] passing unbiased_state to DTRAM class
commit 3b85004d7b5c88ac2e0c896092220eaaad5ff05c
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Tue May 16 15:05:22 2017 +0200
[thermo] adding docstrings to eigenvector methods
commit 6c9aa4d535e55c42cb5e7bc04ae057c06f7a7621
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Mon May 15 19:47:22 2017 -0500
fix tests
commit 799458679e469c4c85b0f947142c5522b29e748e
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Mon May 15 19:41:45 2017 -0500
[streaming-transformer] removed deprecated parametrize method.
commit 8a8a31c9a42859ea3998d7412c0950072c3a24e7
Merge: d1725c67 157152a3
Author: noe <frank.noe@fu-berlin.de>
Date: Tue May 16 02:33:32 2017 +0200
Merge branch 'vamp_crossvalidation' of https://github.com/markovmodel/pyemma into vamp_crossvalidation
Conflicts:
pyemma/msm/estimators/maximum_likelihood_msm.py
commit d1725c67d757da47076aed3c9d4bbf5e1600e391
Author: noe <frank.noe@fu-berlin.de>
Date: Sun May 14 20:23:47 2017 +0200
Added tests for score function
commit fe16747515940945e0861bb1476001fb3708fea2
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Mon May 15 18:16:53 2017 -0500
[conda-recipe] enable warnings reporting.
commit 3644eb93c16ea44fba68ee3e4bbfb9bf6b71735a
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Mon May 15 18:15:57 2017 -0500
[coordinates/tests] removed calls to deprecated func parametrize.
Fixes #1086
commit 157152a3ee992ad2adbd7b02afca337a259d3934
Author: noe <frank.noe@fu-berlin.de>
Date: Sun May 14 20:23:47 2017 +0200
fixed variational metric problems
commit 7596f1a6db5af1dd9f2d29538aa9c4c35a49f17f
Author: noe <frank.noe@fu-berlin.de>
Date: Fri May 12 20:36:09 2017 +0200
Implemented VAMP scores and crossvalidation for MSMs
commit 203482d0683e010d8286efca1b6d1ae2609e658a
Merge: c194d7fe 0704332c
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri May 12 12:14:50 2017 -0500
Merge pull request #1085 from marscher/verbose_on_filehandling_errors
[TrajInfoCache] handle exceptions from bogus files.
Upon an error the file name causing the error is being raised,
along with the actual error trying to obtain the length and dimensions.
commit c194d7fe1f844f48585f7add190e588429c223ca
Merge: 7a4eb9bc 048f11d4
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Fri May 12 10:43:39 2017 -0500
Merge pull request #1084 from marscher/kmeans_progress_collect_data
[kmeans] show a progress bar for collection the data
commit 0704332cb0757d69fe7ee61b4ff5f05ab77869bb
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Fri May 12 10:27:59 2017 -0500
fix
commit 18066ee5bc432870981c03d3df3d908e62822136
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 11 19:20:08 2017 -0500
[TrajInfoCache] handle exceptions from bogus files.
The filename which caused the error along with the original exception message
is being raised as IOError to inform the user the file is corrupt.
commit 048f11d4058c70991cf4b71a69e97389a520d030
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 11 13:57:35 2017 -0500
no progress for minibatch kmeans.
commit 49a6124b973d88b6e46883522422953c889db916
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 11 13:37:18 2017 -0500
fix
commit 27b4374ab3c09a96f9d670cfaa6c3eeca4f9cb68
Author: Martin K. Scherer <m.scherer@fu-berlin.de>
Date: Thu May 11 11:15:36 2017 -0500
[kmeans] show a progress bar for collection the data
commit 721c7c97d77bc8e043e6dd3de6576f8066ed64c7
Author: Christoph Wehmeyer <christoph.wehmeyer@fu-berlin.de>
Date: Wed May 10 22:47:41 2017 +0200
[thermo] adding parameter description for unbiased_state to tram() and dtram()
commit 7a4eb9bc821d7c176d6b2f1a6455eb37a5949b6f
Merge: 4ab0d6e6 844388c5
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Wed May 10 14:49:55 2017 -0500
Merge pull request #1080 from markovmodel/fix_import_tica
Fixed missing import in coordinates/transform/tica
commit 4ab0d6e65142f0e62f738446a94ec4045986c96b
Merge: 49f09a79 320d5547
Author: Martin K. Scherer <marscher@users.noreply.github.com>
Date: Wed May 10 11:23:32 2017 -0500
Merge pull request…
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@franknoe You wanted to include this for the next release, right?
please ping me, if when this is ready to go.