Ecosyste.ms: Issues

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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

#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

#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

#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

#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

#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

#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