deeptime-ml/deeptime issues and pull requests

#299 - restrict_to_submodel in TRAMDataset

Issue - State: open - Opened by kterakura about 1 month ago

#298 - Extracting pdb structures

Issue - State: closed - Opened by GSINGH006 about 2 months ago - 2 comments

#297 - Regarding trajectory data

Issue - State: closed - Opened by GSINGH006 2 months ago - 2 comments

#296 - KoopmanWeightingEstimator partial_fit method throws ValueError

Issue - State: closed - Opened by ajcecil64 2 months ago - 2 comments

#295 - numpy2

Pull Request - State: closed - Opened by clonker 2 months ago - 1 comment

#294 - Add Tutorial for Analyzing MD Trajectories Using Deeptime

Pull Request - State: open - Opened by JilsyXavier 3 months ago - 1 comment

#293 - Cross Validation score for MaximumLikelihoodMSMs and BayesianMSMs

Issue - State: closed - Opened by prateekbansal97 4 months ago - 2 comments

#292 - Remove normalize parameter from sindy

Pull Request - State: closed - Opened by clonker 5 months ago - 1 comment

#291 - restrict scikit-learn version

Pull Request - State: closed - Opened by clonker 5 months ago - 1 comment

#290 - Implementation of Girsanov reweighting in deeptime MSM estimator

Pull Request - State: open - Opened by anyschaefer 5 months ago - 9 comments

#289 - Applying TICA to ragged feature vectors

Issue - State: closed - Opened by ryankzhu 8 months ago - 2 comments

#287 - Example/tutorial for dealing with MD trajectories

Issue - State: open - Opened by pojeda 8 months ago - 1 comment

#285 - Does one need identical features to compare between related systems?

Issue - State: closed - Opened by cgseitz 10 months ago - 4 comments

#283 - deeptime cannot be installed on Mac computers with Apple Silicon and Python 3.12.0.

Issue - State: open - Opened by GuangchenJ 12 months ago - 4 comments

#282 - Which version of VAMPNets is there?

Issue - State: open - Opened by palominohernandez about 1 year ago - 1 comment

#281 - Installation without conda and pip

Issue - State: open - Opened by Owen2015 about 1 year ago - 3 comments

#280 - unify progress callback signature with tqdm

Pull Request - State: closed - Opened by clonker about 1 year ago - 1 comment

#279 - How to compute any actual quantity of the coarse-grained kinetics with employing the fuzzy memberships?

Issue - State: open - Opened by ShenWenHuibit about 1 year ago - 7 comments

#278 - Bayesian Markov models give different MFPT

Issue - State: closed - Opened by ShenWenHuibit about 1 year ago

#277 - VAMPnet gives highly fluctuating score results

Issue - State: closed - Opened by ShenWenHuibit about 1 year ago - 1 comment

#276 - add test for issue#275

Pull Request - State: closed - Opened by clonker about 1 year ago - 1 comment

#275 - [Bug] At least one of the given states is not contained in this model

Issue - State: closed - Opened by DanielWicz about 1 year ago - 2 comments

#274 - detach inverse in the VAMPE score

Pull Request - State: open - Opened by DanielWicz over 1 year ago - 4 comments

#273 - update ci for newer catch2 version and remove conan

Pull Request - State: closed - Opened by clonker over 1 year ago - 1 comment

#272 - Update parallel function according to documentation

Pull Request - State: closed - Opened by SianXiaoCHN over 1 year ago - 2 comments

#271 - Implied timescales from deeptime.decomposition.TICA

Issue - State: closed - Opened by fwaibl over 1 year ago - 2 comments

#270 - Handling parallel simulations

Issue - State: closed - Opened by SianXiaoCHN over 1 year ago - 1 comment

#269 - About applying Deeptime to molecular dynamics simulation trajectories on protien

Issue - State: closed - Opened by TianmingQu over 1 year ago - 3 comments

#268 - cibuildwheel cleanup

Pull Request - State: closed - Opened by clonker almost 2 years ago - 1 comment

#267 - Update for scikit-learn 1.2

Pull Request - State: closed - Opened by clonker almost 2 years ago - 1 comment

#266 - Remove sklearn-private pprint.

Pull Request - State: closed - Opened by clonker almost 2 years ago

#265 - Error importing deeptime with scikit-learn 1.2.0

Issue - State: closed - Opened by stefdoerr almost 2 years ago - 4 comments

#264 - pyproject.toml config

Pull Request - State: closed - Opened by clonker almost 2 years ago - 1 comment

#263 - Enable python 3.11 in CI pipelines

Pull Request - State: closed - Opened by clonker almost 2 years ago - 1 comment

#262 - Added an optional argument for specifying the tolerance in is_reversi…

Pull Request - State: closed - Opened by wehs7661 almost 2 years ago - 2 comments

#261 - Lorenz system, Thomas attractor, Improvements regarding documentation, TV Derivative improvements

Pull Request - State: closed - Opened by clonker almost 2 years ago - 1 comment

#260 - TV derivative and minor documentation fixes

Pull Request - State: closed - Opened by clonker almost 2 years ago - 1 comment

#259 - Allowing weights for VAMP dimensionality reduction

Issue - State: open - Opened by jdrusso about 2 years ago - 6 comments

#258 - Remove deprecated CK Test validator

Pull Request - State: closed - Opened by clonker about 2 years ago - 1 comment

#257 - remove print

Pull Request - State: closed - Opened by MaaikeG about 2 years ago - 1 comment

#256 - Automate generating bdist wheels

Issue - State: closed - Opened by clonker about 2 years ago - 1 comment
Labels: enhancement, continuous-integration

#255 - Var_cutoff can be disabled in covariance koopman models. Fixes #254.

Pull Request - State: closed - Opened by clonker about 2 years ago - 1 comment

#254 - TICA fit-once transform-many

Issue - State: closed - Opened by stefdoerr about 2 years ago - 6 comments

#251 - Error when installing from local repo via pip

Issue - State: closed - Opened by abittracher about 2 years ago - 4 comments

#250 - [setup] exclude examples, docs, devtools when packaging

Pull Request - State: closed - Opened by clonker about 2 years ago

#249 - py38

Pull Request - State: closed - Opened by clonker about 2 years ago - 1 comment

#248 - Cannot install deeptime. I have Python 3.10 (Windows 10) and trying to install using Visual Studio 2022

Issue - State: closed - Opened by panandreou about 2 years ago - 12 comments

#247 - Contour and density plot utility functions

Pull Request - State: closed - Opened by clonker about 2 years ago - 1 comment

#246 - Fix the bug

Pull Request - State: closed - Opened by MaaikeG about 2 years ago - 1 comment

#245 - Convergence warning bugfix

Pull Request - State: closed - Opened by MaaikeG about 2 years ago - 2 comments

#244 - [ci] fix python 3.8

Pull Request - State: closed - Opened by clonker about 2 years ago - 1 comment

#243 - better error handling for trajectories dataset

Pull Request - State: closed - Opened by clonker about 2 years ago - 1 comment

#242 - proper exception handling in trajectory-generating openmp block

Pull Request - State: closed - Opened by clonker about 2 years ago - 3 comments

#241 - Better error handling for custom_sde

Issue - State: closed - Opened by thempel over 2 years ago
Labels: low-prio

#240 - Fix preprocess data call in SINDy

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#239 - Fix shape of empty count models

Pull Request - State: closed - Opened by MaaikeG over 2 years ago - 1 comment

#238 - TrajectoriesDataset misleading error message

Issue - State: closed - Opened by thempel over 2 years ago

#237 - plot fluxes

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#236 - Network plots

Pull Request - State: closed - Opened by clonker over 2 years ago - 2 comments

#235 - Units

Issue - State: open - Opened by clonker over 2 years ago
Labels: enhancement

#234 - plot energy surfaces

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#233 - CI: Update manifest to include npz data files, don't use editable install for nox make_docs

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#232 - update manifest to include cmakelists

Pull Request - State: closed - Opened by clonker over 2 years ago

#231 - Fix in setup

Pull Request - State: closed - Opened by clonker over 2 years ago

#230 - update project metadata

Pull Request - State: closed - Opened by clonker over 2 years ago

#229 - [datasets] correct 1D triple well docs

Pull Request - State: closed - Opened by thempel over 2 years ago - 1 comment

#228 - Update versioneer and run cython from CMake

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#227 - Versioneer update

Pull Request - State: closed - Opened by clonker over 2 years ago

#226 - pyproject.toml: use dynamic version

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#224 - Build fails suddenly

Issue - State: closed - Opened by cap-jmk over 2 years ago - 3 comments

#223 - Small doc fixes and update testing dependencies

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#222 - Disable TF-32 tensor cores for VAMPNET training

Pull Request - State: closed - Opened by yuxuanzhuang over 2 years ago - 3 comments

#221 - typos in _koopman.py

Pull Request - State: closed - Opened by KirillShmilovich over 2 years ago - 2 comments

#220 - Different VAMPNET results from CPU/GPU training

Issue - State: closed - Opened by yuxuanzhuang over 2 years ago - 11 comments

#219 - Fix bug in statdist caching for msms

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#218 - Sort Markov matrix

Issue - State: open - Opened by cap-jmk over 2 years ago - 21 comments

#217 - Tram experiments

Pull Request - State: closed - Opened by MaaikeG over 2 years ago - 1 comment

#216 - use Agg backend in plotting tests

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#215 - Use CMake as primary build system via scikit-build

Pull Request - State: closed - Opened by clonker over 2 years ago - 3 comments

#214 - Tram experiments

Pull Request - State: closed - Opened by MaaikeG over 2 years ago - 1 comment

#213 - Docs update

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#212 - Installation runs into CUDA problem

Issue - State: closed - Opened by cap-jmk over 2 years ago - 13 comments

#211 - add device option for TAE class

Pull Request - State: closed - Opened by philipyoung9561 over 2 years ago - 2 comments

#210 - new tram notebook version

Pull Request - State: closed - Opened by MaaikeG over 2 years ago - 1 comment

#209 - fix the big bad bug

Pull Request - State: closed - Opened by MaaikeG over 2 years ago - 1 comment

#208 - Minor changes

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#207 - Mbar initialization for tram

Pull Request - State: closed - Opened by MaaikeG over 2 years ago - 1 comment

#206 - Fix the calculation of the PMF.

Pull Request - State: closed - Opened by MaaikeG over 2 years ago - 1 comment

#205 - Update validation loss on TAE

Pull Request - State: closed - Opened by clarktemple03 over 2 years ago - 2 comments

#204 - Fix numpy deprecated warning

Pull Request - State: closed - Opened by MaaikeG over 2 years ago - 2 comments

#203 - Chapman-Kolmogorov test for Koopman models

Issue - State: open - Opened by clonker over 2 years ago
Labels: enhancement

#202 - New Chapman-Kolmogorov test implementation

Pull Request - State: closed - Opened by clonker over 2 years ago - 1 comment

#201 - Make sample weights normalized

Pull Request - State: closed - Opened by MaaikeG over 2 years ago - 2 comments

GitHub / deeptime-ml/deeptime issues and pull requests