Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / openpathsampling/openpathsampling issues and pull requests
#1148 - Update 2.0 after release of 1.6.1
Pull Request -
State: closed - Opened by dwhswenson about 2 months ago
- 1 comment
Labels: 2.0
#1147 - Bump 1.6.2.dev0
Pull Request -
State: closed - Opened by dwhswenson 2 months ago
#1146 - OpenPathSampling 1.6.1
Pull Request -
State: closed - Opened by dwhswenson 2 months ago
- 2 comments
#1145 - Test against Python 3.12; deprecate PyEMMA
Pull Request -
State: closed - Opened by dwhswenson 2 months ago
- 1 comment
Labels: misc PR, Deprecations
#1143 - MDTrajFunctionCV implicit trajectory conversion fails
Issue -
State: open - Opened by Bernadette-Mohr 4 months ago
#1142 - Fix a few more setup -> setup_method tests
Pull Request -
State: closed - Opened by dwhswenson 5 months ago
- 3 comments
Labels: misc PR, upstream changed
#1141 - Cut off `nose`
Pull Request -
State: closed - Opened by dwhswenson 6 months 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 6 months ago
#1139 - Bump 1.6.1.dev0
Pull Request -
State: closed - Opened by dwhswenson 6 months ago
- 1 comment
#1138 - Release 1.6.0
Pull Request -
State: closed - Opened by dwhswenson 6 months ago
- 2 comments
#1137 - Fix engine props for OpenMM 8.1
Pull Request -
State: closed - Opened by dwhswenson 6 months ago
- 1 comment
Labels: misc PR, upstream changed
#1136 - Pin nbval != 0.10.0
Pull Request -
State: closed - Opened by dwhswenson 8 months 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 9 months ago
- 3 comments
#1134 - Update pins
Pull Request -
State: closed - Opened by dwhswenson 9 months ago
- 1 comment
Labels: misc PR
#1133 - Support Python 3.10; Python 3.11
Pull Request -
State: closed - Opened by dwhswenson 10 months ago
- 1 comment
Labels: misc PR
#1132 - Get tests working again
Pull Request -
State: closed - Opened by dwhswenson 10 months ago
- 1 comment
Labels: misc PR
#1131 - SimStore data loss after crash
Issue -
State: open - Opened by Bernadette-Mohr 11 months ago
- 7 comments
#1130 - Updates for SQLAlchemy 2.0
Pull Request -
State: closed - Opened by dwhswenson over 1 year ago
- 2 comments
Labels: misc PR, upstream changed
#1129 - Fix testing against OpenMM RCs
Pull Request -
State: closed - Opened by dwhswenson over 1 year ago
- 2 comments
Labels: misc PR
#1128 - Fix Dropbox download of precalculated results
Pull Request -
State: closed - Opened by dwhswenson over 1 year ago
- 2 comments
Labels: misc PR
#1127 - Unpin numpy when possible
Issue -
State: open - Opened by dwhswenson over 1 year ago
#1126 - Temporary pin: numpy<1.24
Pull Request -
State: closed - Opened by dwhswenson over 1 year ago
- 1 comment
Labels: misc PR
#1125 - Test failures (due to llvm change?)
Issue -
State: closed - Opened by dwhswenson over 1 year ago
#1124 - TPS accepts non-transitions paths too
Issue -
State: open - Opened by gyorgy-hantal over 1 year ago
#1123 - update tests to use setup_method instead of setup, same for teardown
Pull Request -
State: closed - Opened by sroet over 1 year ago
- 1 comment
Labels: misc PR
#1122 - clarify error message on missing units
Pull Request -
State: closed - Opened by dwhswenson over 1 year ago
- 1 comment
Labels: misc PR
#1121 - Questions about running TPS+U simulation in OPS framework
Issue -
State: open - Opened by smlee99 almost 2 years ago
- 2 comments
#1120 - Subtrajectories issue
Issue -
State: closed - Opened by smlee99 almost 2 years ago
- 5 comments
#1119 - [WIP] engine_masses feature; use in Gromacs engine
Pull Request -
State: open - Opened by dwhswenson almost 2 years ago
- 4 comments
#1118 - [WIP] Fail fast if `prepare` fails in external engines
Pull Request -
State: open - Opened by dwhswenson almost 2 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 2 years ago
- 6 comments
#1116 - Use MDTraj codecs in SimStore JSON serialization
Pull Request -
State: closed - Opened by dwhswenson almost 2 years ago
Labels: bugfix, experimental
#1115 - run_until_decorrelated();TypeError: iteration over a 0-d array
Issue -
State: open - Opened by ShenWenHuibit almost 2 years ago
- 22 comments
#1114 - (Possible temporary) Fix dill in testing
Pull Request -
State: closed - Opened by dwhswenson about 2 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 2 years ago
- 2 comments
#1112 - Dill 0.3.5 causes problems in test suite
Issue -
State: closed - Opened by dwhswenson about 2 years ago
#1111 - Setting up TPS calculations starting from transition paths generated by TIS fails
Issue -
State: open - Opened by gyorgy-hantal about 2 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 about 2 years ago
- 8 comments
Labels: misc PR
#1109 - Prevent double monkey-patching experimental storage
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 3 comments
Labels: bugfix, experimental
#1108 - Experimental Storage fails at reloading
Issue -
State: open - Opened by gianmarcolazzeri over 2 years ago
- 3 comments
#1107 - retis not restarting from preset trajectory number
Issue -
State: closed - Opened by gyorgy-hantal over 2 years ago
- 6 comments
#1106 - revert openmmtools import guard from test notebook
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 2 comments
Labels: misc PR
#1105 - resolve Issue 1101
Pull Request -
State: open - Opened by sroet over 2 years ago
- 1 comment
#1104 - accessing the website via https instead of http times out (also the main website from FF private window)
Issue -
State: open - Opened by sroet over 2 years ago
- 1 comment
#1103 - Update standard filename setter for external engines in OPS 2.0
Pull Request -
State: open - Opened by sroet over 2 years ago
- 2 comments
Labels: 2.0
#1102 - Add FutureWarning for default filesetter external engines
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 1 comment
Labels: misc PR, Deprecations
#1101 - Continuing a Path Sampling Simulation with GROMACS
Issue -
State: open - Opened by jjfsteuer over 2 years ago
- 7 comments
#1100 - Move check-openmm-rc off of main branch
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 3 comments
Labels: misc PR
#1099 - Trajectories should be deque, not lists (while generating)
Issue -
State: open - Opened by sroet over 2 years ago
- 3 comments
#1098 - The store cannot hold snapshots of the given type
Issue -
State: open - Opened by KeweiZhao over 2 years ago
- 1 comment
#1097 - update copyright to 2022
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 3 comments
Labels: misc PR
#1096 - make a missed string into a rawstring
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 2 comments
Labels: misc PR
#1095 - Python 3.10 checklist
Issue -
State: open - Opened by dwhswenson over 2 years ago
#1094 - enable py310 tests
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 9 comments
#1093 - Fix build for OpenMM RCs
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 3 comments
Labels: misc PR
#1092 - Actually check for CVDefinedVolume.lambda_max == "inf"
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 2 comments
Labels: bugfix
#1091 - Guard against openmm import warnings (including those from OpenMMTools)
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 7 comments
Labels: misc PR
#1090 - Docs: New Installation docs
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 1 comment
Labels: misc PR, docs
#1089 - Bump to Autorelease 0.3.2
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 2 comments
Labels: misc PR
#1088 - SimStore: Fix storable function serialization
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 2 comments
Labels: bugfix, experimental
#1087 - DOCS: Add GitHub support to `copyfiles`, remove online notebook downloads
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 1 comment
Labels: misc PR, docs
#1086 - SimStore: Fix issue with internalized snapshot box vectors
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 1 comment
Labels: bugfix, experimental
#1085 - OpenMMEngine: use masses from mdtraj topolgy directly
Pull Request -
State: closed - Opened by hejung over 2 years ago
- 3 comments
Labels: bugfix
#1084 - openMM snapshot.masses fails for snapshots with TopologyEngine and virtual sites
Issue -
State: closed - Opened by hejung over 2 years ago
- 5 comments
Labels: bug report
#1083 - Fix website issues for Sphinx RTD Theme 1.0
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 3 comments
Labels: misc PR, docs
#1082 - unbreak API call to selector.probability_ratio
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 1 comment
Labels: bugfix
#1081 - Python versions should be strings in YAML
Pull Request -
State: closed - Opened by dwhswenson over 2 years ago
- 2 comments
Labels: misc PR
#1080 - Hashing, Equality, and UUIDs in OPS 2.0
Issue -
State: open - Opened by dwhswenson over 2 years ago
- 2 comments
Labels: 2.0, discussion
#1079 - add no_copy option to NoModifier and Deprecate 'subset_mask'
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 4 comments
Labels: enhancement
#1078 - swap codecov bash uploader to github action
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 3 comments
Labels: misc PR
#1077 - Swap to v2 of the codecov github action
Issue -
State: closed - Opened by sroet over 2 years ago
#1076 - Take care of coordinate modifcation in selector probability_ratio
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 7 comments
Labels: enhancement
#1075 - Account for modifier acceptance in engine movers
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 10 comments
Labels: enhancement
#1074 - conda_ops_dev_install.sh failing on miniconda3 docker image
Issue -
State: closed - Opened by sroet over 2 years ago
- 2 comments
#1073 - Switch CI install to mamba
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 3 comments
Labels: misc PR
#1072 - Switch CI install to mamba
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 4 comments
#1071 - Switch CI install to mamba
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 2 comments
Labels: misc PR
#1070 - [TODO] Unpin GitPython
Issue -
State: closed - Opened by dwhswenson almost 3 years ago
- 1 comment
#1069 - Temporary pin for GitPython
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 3 comments
#1068 - New analysis testing utilities
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 5 comments
Labels: enhancement
#1067 - Does OPS officially support pypi?
Issue -
State: closed - Opened by sroet almost 3 years ago
- 1 comment
#1066 - Clear old ExternalMDSnapshots during `iter_generate`
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 4 comments
Labels: enhancement
#1065 - improvements to unpatch after using SimStore
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 1 comment
Labels: misc PR, experimental
#1064 - Add CITATIONS.md
Pull Request -
State: closed - Opened by sroet almost 3 years ago
- 5 comments
Labels: misc PR
#1063 - Add citation to the repo
Issue -
State: closed - Opened by sroet almost 3 years ago
#1062 - Limit nightly CI and release/deployment CI to the base repository (not forks).
Pull Request -
State: closed - Opened by bdice almost 3 years ago
- 4 comments
#1061 - Nightly tests / release workflows failing on forks
Issue -
State: open - Opened by bdice almost 3 years ago
- 1 comment
#1060 - [WIP] Add HOOMD Engine
Pull Request -
State: closed - Opened by bdice almost 3 years ago
- 2 comments
Labels: feature
#1059 - [WIP] New "snapshot features" implementation
Pull Request -
State: open - Opened by dwhswenson almost 3 years ago
- 6 comments
Labels: 2.0
#1058 - Remove engine binary after tests
Pull Request -
State: closed - Opened by sroet almost 3 years ago
- 1 comment
Labels: misc PR
#1057 - Fix documentation issues
Pull Request -
State: closed - Opened by bdice almost 3 years ago
- 2 comments
Labels: misc PR, docs
#1056 - Bump version to 1.5.3.dev0
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 1 comment
#1055 - Adding support for HOOMD-blue simulation engine
Issue -
State: open - Opened by bdice almost 3 years ago
- 3 comments
#1054 - OpenPathSampling 1.5.2
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 2 comments
#1053 - OpenPathSampling 1.5.2
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 3 comments
#1052 - Prevent non-string names in StorableNamedObject
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 1 comment
Labels: misc PR
#1051 - Fixes for OpenMM 7.6 RC
Pull Request -
State: closed - Opened by dwhswenson almost 3 years ago
- 4 comments
Labels: misc PR, upstream changed
#1050 - add simstore table access via slice
Pull Request -
State: closed - Opened by sroet almost 3 years ago
- 5 comments
Labels: enhancement, experimental
#1049 - API 2.0: Improve parameters in existing code
Issue -
State: open - Opened by dwhswenson almost 3 years ago
- 4 comments
Labels: 2.0
#1048 - [WIP] New path tree
Pull Request -
State: open - Opened by dwhswenson almost 3 years ago
- 2 comments