openpathsampling/openpathsampling issues and pull requests

#1174 - Drop numpy pin

Pull Request - State: closed - Opened by dwhswenson about 2 months ago - 2 comments
Labels: misc PR, ci

#1173 - Use `autorelease check` instead of custom script

Pull Request - State: closed - Opened by dwhswenson 3 months ago - 2 comments
Labels: misc PR, ci

#1172 - Trajectory Exports: MDTraj and TRR formats; Gromacs and OpenMM support

Pull Request - State: closed - Opened by dwhswenson 7 months ago - 2 comments
Labels: enhancement

#1171 - Significant difference in pickle file sizes containing CV trajectories, depending on source of CV functions

Issue - State: open - Opened by Bernadette-Mohr 7 months ago - 1 comment

#1170 - Trajectory Exports: Core and integration in `DynamicsEngine`

Pull Request - State: closed - Opened by dwhswenson 7 months ago - 2 comments
Labels: enhancement

#1169 - Update for SPEC0 as of Dec 2024

Pull Request - State: open - Opened by dwhswenson 7 months ago - 9 comments
Labels: misc PR, ci

#1168 - RETIS evaluation fails with the new storage files

Issue - State: open - Opened by gyorgy-hantal 8 months ago

#1167 - [WIP] Checkpointing, part 1

Pull Request - State: open - Opened by dwhswenson 9 months ago

#1163 - Update to use setup-miniconda v3; use miniforge

Pull Request - State: closed - Opened by dwhswenson 10 months ago - 2 comments
Labels: misc PR, ci

#1162 - ERROR in: scheme.initial_conditions_from_trajectories()

Issue - State: closed - Opened by SesswireD 10 months ago - 9 comments

#1161 - Bump 1.7.1.dev0

Pull Request - State: closed - Opened by dwhswenson 10 months ago - 1 comment

#1160 - Release 1.7.0

Pull Request - State: closed - Opened by dwhswenson 10 months ago - 2 comments

#1159 - CLI `compile` docs

Pull Request - State: closed - Opened by dwhswenson 10 months ago - 2 comments
Labels: misc PR, docs

#1158 - Storage Interfaces

Pull Request - State: closed - Opened by dwhswenson 11 months ago - 2 comments
Labels: enhancement

#1157 - SimStore performance improvements and fixes

Pull Request - State: closed - Opened by dwhswenson 11 months ago - 2 comments
Labels: enhancement, experimental

#1156 - Update to CodeCov v4 (using CODECOV_TOKEN secret)

Pull Request - State: closed - Opened by dwhswenson 12 months ago - 2 comments
Labels: misc PR

#1155 - Let UUID determine equality for ensembles

Pull Request - State: closed - Opened by dwhswenson 12 months ago - 2 comments
Labels: misc PR

#1154 - Custom `PathDensityHistogram._add_ops_trajectory`

Pull Request - State: closed - Opened by dwhswenson 12 months ago - 2 comments
Labels: enhancement, refactor

#1153 - Fix `SQLStorageBackend.load_storable_function_table`

Pull Request - State: closed - Opened by dwhswenson 12 months ago - 2 comments
Labels: bugfix, experimental

#1152 - `psutil.AccessDenied` error in CI

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

#1151 - Volume shooting point selector

Pull Request - State: closed - Opened by dwhswenson about 1 year ago - 1 comment
Labels: enhancement

#1150 - Fix histogram xvals

Pull Request - State: closed - Opened by dwhswenson about 1 year ago - 1 comment
Labels: bugfix

#1149 - Update Python version in test-openmm-rc

Pull Request - State: closed - Opened by dwhswenson about 1 year ago - 3 comments
Labels: misc PR

#1148 - Update 2.0 after release of 1.6.1

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment
Labels: 2.0

#1147 - Bump 1.6.2.dev0

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

#1146 - OpenPathSampling 1.6.1

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

#1145 - Test against Python 3.12; deprecate PyEMMA

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment
Labels: misc PR, Deprecations

#1143 - MDTrajFunctionCV implicit trajectory conversion fails

Issue - State: open - Opened by Bernadette-Mohr over 1 year ago

#1142 - Fix a few more setup -> setup_method tests

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 3 comments
Labels: misc PR, upstream changed

#1141 - Cut off `nose`

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 3 comments
Labels: misc PR, upstream changed

#1140 - Python 3.12 breaks `nose`; all `nose` based testing should be removed

Issue - State: closed - Opened by dwhswenson over 1 year ago

#1139 - Bump 1.6.1.dev0

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

#1138 - Release 1.6.0

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

#1137 - Fix engine props for OpenMM 8.1

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment
Labels: misc PR, upstream changed

#1136 - Pin nbval != 0.10.0

Pull Request - State: closed - Opened by dwhswenson almost 2 years ago - 2 comments
Labels: misc PR

#1135 - OPS cannot access stored OP values in database during RETIS analysis

Issue - State: open - Opened by gyorgy-hantal almost 2 years ago - 3 comments

#1134 - Update pins

Pull Request - State: closed - Opened by dwhswenson almost 2 years ago - 1 comment
Labels: misc PR

#1133 - Support Python 3.10; Python 3.11

Pull Request - State: closed - Opened by dwhswenson almost 2 years ago - 1 comment
Labels: misc PR

#1132 - Get tests working again

Pull Request - State: closed - Opened by dwhswenson almost 2 years ago - 1 comment
Labels: misc PR

#1131 - SimStore data loss after crash

Issue - State: open - Opened by Bernadette-Mohr almost 2 years ago - 7 comments

#1130 - Updates for SQLAlchemy 2.0

Pull Request - State: closed - Opened by dwhswenson over 2 years ago - 2 comments
Labels: misc PR, upstream changed

#1129 - Fix testing against OpenMM RCs

Pull Request - State: closed - Opened by dwhswenson over 2 years ago - 2 comments
Labels: misc PR

#1128 - Fix Dropbox download of precalculated results

Pull Request - State: closed - Opened by dwhswenson over 2 years ago - 2 comments
Labels: misc PR

#1127 - Unpin numpy when possible

Issue - State: open - Opened by dwhswenson over 2 years ago

#1126 - Temporary pin: numpy<1.24

Pull Request - State: closed - Opened by dwhswenson over 2 years ago - 1 comment
Labels: misc PR

#1125 - Test failures (due to llvm change?)

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

#1124 - TPS accepts non-transitions paths too

Issue - State: open - Opened by gyorgy-hantal over 2 years ago

#1123 - update tests to use setup_method instead of setup, same for teardown

Pull Request - State: closed - Opened by sroet over 2 years ago - 1 comment
Labels: misc PR

#1122 - clarify error message on missing units

Pull Request - State: closed - Opened by dwhswenson almost 3 years ago - 1 comment
Labels: misc PR

#1121 - Questions about running TPS+U simulation in OPS framework

Issue - State: open - Opened by smlee99 almost 3 years ago - 2 comments

#1120 - Subtrajectories issue

Issue - State: closed - Opened by smlee99 almost 3 years ago - 5 comments

#1119 - [WIP] engine_masses feature; use in Gromacs engine

Pull Request - State: open - Opened by dwhswenson almost 3 years ago - 4 comments

#1118 - [WIP] Fail fast if `prepare` fails in external engines

Pull Request - State: open - Opened by dwhswenson almost 3 years ago - 1 comment

#1117 - Upon doing Alanine Dipeptide tutorial given on openpathsampling website, I have faced a error in the CommittorSimulation

Issue - State: open - Opened by skhabib388 almost 3 years ago - 6 comments

#1116 - Use MDTraj codecs in SimStore JSON serialization

Pull Request - State: closed - Opened by dwhswenson almost 3 years ago
Labels: bugfix, experimental

#1115 - run_until_decorrelated();TypeError: iteration over a 0-d array

Issue - State: open - Opened by ShenWenHuibit about 3 years ago - 22 comments

#1114 - (Possible temporary) Fix dill in testing

Pull Request - State: closed - Opened by dwhswenson about 3 years ago - 1 comment
Labels: misc PR, upstream changed

#1113 - [DO NOT MERGE] install experimental dill fix

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

#1112 - Dill 0.3.5 causes problems in test suite

Issue - State: closed - Opened by dwhswenson about 3 years ago

#1111 - Setting up TPS calculations starting from transition paths generated by TIS fails

Issue - State: open - Opened by gyorgy-hantal over 3 years ago - 6 comments

#1110 - Improved implementation of shooting point selector pick (avoid model that might introduce index error in subclasses)

Pull Request - State: closed - Opened by hejung over 3 years ago - 8 comments
Labels: misc PR

GitHub / openpathsampling/openpathsampling issues and pull requests