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Title: SimStore part 2: Storable functions (and more) by dwhswenson · Pull Request #929 · openpathsampling/openpathsampling · GitHub

Open Graph Title: SimStore part 2: Storable functions (and more) by dwhswenson · Pull Request #929 · openpathsampling/openpathsampling

X Title: SimStore part 2: Storable functions (and more) by dwhswenson · Pull Request #929 · openpathsampling/openpathsampling

Description: This is the second PR in the process of updating the OPS storage subsystem, following on #928. See #928 for overall motivation. Major improvements in this PR: StorableFunction: a new base class f...

Open Graph Description: This is the second PR in the process of updating the OPS storage subsystem, following on #928. See #928 for overall motivation. Major improvements in this PR: StorableFunction: a new base class f...

X Description: This is the second PR in the process of updating the OPS storage subsystem, following on #928. See #928 for overall motivation. Major improvements in this PR: StorableFunction: a new base class f...

Opengraph URL: https://github.com/openpathsampling/openpathsampling/pull/929

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og:image:altThis is the second PR in the process of updating the OPS storage subsystem, following on #928. See #928 for overall motivation. Major improvements in this PR: StorableFunction: a new base class f...
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dwhswenson:storable_functionshttps://github.com/dwhswenson/openpathsampling/tree/storable_functions
SimStore part 2: Storable functions (and more) https://github.com/openpathsampling/openpathsampling/pull/929#top
dwhswensonhttps://github.com/dwhswenson
openpathsampling:masterhttps://github.com/openpathsampling/openpathsampling/tree/master
dwhswenson:storable_functionshttps://github.com/dwhswenson/openpathsampling/tree/storable_functions
Conversation 1 https://github.com/openpathsampling/openpathsampling/pull/929
Commits 37 https://github.com/openpathsampling/openpathsampling/pull/929/commits
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Sep 25, 2020https://github.com/openpathsampling/openpathsampling/pull/929#issue-708853499
Please reload this pagehttps://github.com/openpathsampling/openpathsampling/pull/929
#928https://github.com/openpathsampling/openpathsampling/pull/928
#928https://github.com/openpathsampling/openpathsampling/pull/928
#928https://github.com/openpathsampling/openpathsampling/pull/928
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dwhswensonhttps://github.com/dwhswenson
September 19, 2019 15:59https://github.com/openpathsampling/openpathsampling/pull/929#commits-pushed-902dcff
https://github.com/dwhswenson
Add callable codec and testshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/902dcff4a2cf0189cc017380dd448f32e8a0ceb4
902dcffhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/902dcff4a2cf0189cc017380dd448f32e8a0ceb4
https://github.com/dwhswenson
sql backend for storable functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/69782cb60386fd29daf57bd59b7a5d2304bfecac
69782cbhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/69782cb60386fd29daf57bd59b7a5d2304bfecac
https://github.com/dwhswenson
Merge branch 'storage' into storable_functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/2c98789448000bbc9d90e5eb5f5935c720177725
2c98789https://github.com/openpathsampling/openpathsampling/pull/929/commits/2c98789448000bbc9d90e5eb5f5935c720177725
https://github.com/dwhswenson
Merge remote-tracking branch 'upstream/master' into storable_functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/e578985fee026a57d16e68f85a55c2d7b0d59847
e578985https://github.com/openpathsampling/openpathsampling/pull/929/commits/e578985fee026a57d16e68f85a55c2d7b0d59847
https://github.com/dwhswenson
Basic storable funcshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/b1110c38383f43a0e5bacce09190bde642546e84
b1110c3https://github.com/openpathsampling/openpathsampling/pull/929/commits/b1110c38383f43a0e5bacce09190bde642546e84
https://github.com/dwhswenson
Steps toward "gather" for StorableFunctionResultshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/f0ced8582e8fa0a644a6635c0486a3371a8a5ae4
f0ced85https://github.com/openpathsampling/openpathsampling/pull/929/commits/f0ced8582e8fa0a644a6635c0486a3371a8a5ae4
https://github.com/dwhswenson
can reload storable funcs from storagehttps://github.com/openpathsampling/openpathsampling/pull/929/commits/baec27f49fcbf4d3ee6f3f5831bf108b9aca2d9b
baec27fhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/baec27f49fcbf4d3ee6f3f5831bf108b9aca2d9b
https://github.com/dwhswenson
Add preload cache; support for parallel CV gatherhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/ecd144cd71c8732389a1fef9046c8610eff9a29f
ecd144chttps://github.com/openpathsampling/openpathsampling/pull/929/commits/ecd144cd71c8732389a1fef9046c8610eff9a29f
https://github.com/dwhswenson
storable funcs now seem to work!https://github.com/openpathsampling/openpathsampling/pull/929/commits/deac34fdb3d9855982568d13c02224f7fa179b57
deac34fhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/deac34fdb3d9855982568d13c02224f7fa179b57
https://github.com/dwhswenson
start to StorableFunctionConfighttps://github.com/openpathsampling/openpathsampling/pull/929/commits/28e50649cad9417551b4a008ae5de6ca60dfe176
28e5064https://github.com/openpathsampling/openpathsampling/pull/929/commits/28e50649cad9417551b4a008ae5de6ca60dfe176
https://github.com/dwhswenson
I think this is working StorableFuncConfighttps://github.com/openpathsampling/openpathsampling/pull/929/commits/0c1cf23ce7bb5f1fcbef0914c8acab354d71cd77
0c1cf23https://github.com/openpathsampling/openpathsampling/pull/929/commits/0c1cf23ce7bb5f1fcbef0914c8acab354d71cd77
https://github.com/dwhswenson
Tests for StorageFunctionHandlerhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/d583e79f3602b3053035afc6b5c49784dde190c4
d583e79https://github.com/openpathsampling/openpathsampling/pull/929/commits/d583e79f3602b3053035afc6b5c49784dde190c4
https://github.com/dwhswenson
Add CVs, including MDTrajFunctionCVhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/59942a0c1c573fc8255733598d0c503110d6fd1e
59942a0https://github.com/openpathsampling/openpathsampling/pull/929/commits/59942a0c1c573fc8255733598d0c503110d6fd1e
https://github.com/dwhswenson
Add SimStore support to ExternalMDSnapshothttps://github.com/openpathsampling/openpathsampling/pull/929/commits/36654d56f76f50a8fa810d0ccc43de5b3a66ed67
36654d5https://github.com/openpathsampling/openpathsampling/pull/929/commits/36654d56f76f50a8fa810d0ccc43de5b3a66ed67
https://github.com/dwhswenson
fixes to get Gromacs traj running with SimStorehttps://github.com/openpathsampling/openpathsampling/pull/929/commits/0afac9ef9f277465c0ea9bbfa2d9620afca241d3
0afac9ehttps://github.com/openpathsampling/openpathsampling/pull/929/commits/0afac9ef9f277465c0ea9bbfa2d9620afca241d3
https://github.com/dwhswenson
Fixes to test errors introduced in CallableCodechttps://github.com/openpathsampling/openpathsampling/pull/929/commits/26ea3462b77618b467ca19c40eb7e90ca7e67492
26ea346https://github.com/openpathsampling/openpathsampling/pull/929/commits/26ea3462b77618b467ca19c40eb7e90ca7e67492
https://github.com/dwhswenson
Remove unused class_idxhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/21f4cc09cf860ce6e37991e6e436696cd71c4a50
21f4cc0https://github.com/openpathsampling/openpathsampling/pull/929/commits/21f4cc09cf860ce6e37991e6e436696cd71c4a50
https://github.com/dwhswenson
Mostly working memory backend for network xferhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/bf70519c0b5f199ee0e49b3c9104610b30450505
bf70519https://github.com/openpathsampling/openpathsampling/pull/929/commits/bf70519c0b5f199ee0e49b3c9104610b30450505
https://github.com/dwhswenson
Merge remote-tracking branch 'upstream/master' into storable_functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/78dd77f3ed30ceba142b8b598a2cb6c59c913972
78dd77fhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/78dd77f3ed30ceba142b8b598a2cb6c59c913972
https://github.com/dwhswenson
Merge branch 'storage' into storable_functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/dabccfcd98030e0df9e4d319f7ee69d3b99515d1
dabccfchttps://github.com/openpathsampling/openpathsampling/pull/929/commits/dabccfcd98030e0df9e4d319f7ee69d3b99515d1
https://github.com/dwhswenson
Merge branch 'storage' into storable_functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/66a38bef6013a2d9c3e37a7b2ec4f3a97b4c3ef4
66a38behttps://github.com/openpathsampling/openpathsampling/pull/929/commits/66a38bef6013a2d9c3e37a7b2ec4f3a97b4c3ef4
https://github.com/dwhswenson
Changes to make storage objects storablehttps://github.com/openpathsampling/openpathsampling/pull/929/commits/22b63d062f56daf023de57b36c7cf3e8fe586def
22b63d0https://github.com/openpathsampling/openpathsampling/pull/929/commits/22b63d062f56daf023de57b36c7cf3e8fe586def
https://github.com/dwhswenson
Merge branch 'storage' into storable_functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/47d92f8f287abb7325e1488e644d97f87028e383
47d92f8https://github.com/openpathsampling/openpathsampling/pull/929/commits/47d92f8f287abb7325e1488e644d97f87028e383
https://github.com/dwhswenson
fix problem with identifier for sqlite :memory:https://github.com/openpathsampling/openpathsampling/pull/929/commits/3e4ce6113b1dcdfae88eacfb198e5132f69d5276
3e4ce61https://github.com/openpathsampling/openpathsampling/pull/929/commits/3e4ce6113b1dcdfae88eacfb198e5132f69d5276
https://github.com/dwhswenson
Fix a potential bug in saving storage identifiershttps://github.com/openpathsampling/openpathsampling/pull/929/commits/b77319cfd1286dd6ff3bebc27bef8d09c7c3c30e
b77319chttps://github.com/openpathsampling/openpathsampling/pull/929/commits/b77319cfd1286dd6ff3bebc27bef8d09c7c3c30e
https://github.com/dwhswenson
Merge branch 'storage' into storable_functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/52699180d2dd8ddcd771a10818703cd37b94bfb5
5269918https://github.com/openpathsampling/openpathsampling/pull/929/commits/52699180d2dd8ddcd771a10818703cd37b94bfb5
https://github.com/dwhswenson
fix (most) test issues after renaminghttps://github.com/openpathsampling/openpathsampling/pull/929/commits/dc455c75b55e30957301972ec1d5e7cac353b18d
dc455c7https://github.com/openpathsampling/openpathsampling/pull/929/commits/dc455c75b55e30957301972ec1d5e7cac353b18d
https://github.com/dwhswenson
StorageTable no longer takes a cachehttps://github.com/openpathsampling/openpathsampling/pull/929/commits/1513273e23626cc0faa7bfc26c449ecb4f6d9706
1513273https://github.com/openpathsampling/openpathsampling/pull/929/commits/1513273e23626cc0faa7bfc26c449ecb4f6d9706
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Sep 25, 2020 https://github.com/openpathsampling/openpathsampling/pull/929#ref-pullrequest-703682052
SimStore: New storage subsystem (part 1) #928 https://github.com/openpathsampling/openpathsampling/pull/928
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
misc PR https://github.com/openpathsampling/openpathsampling/issues?q=state%3Aopen%20label%3A%22misc%20PR%22
Sep 26, 2020https://github.com/openpathsampling/openpathsampling/pull/929#event-3811104232
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
experimental https://github.com/openpathsampling/openpathsampling/issues?q=state%3Aopen%20label%3Aexperimental
Sep 26, 2020https://github.com/openpathsampling/openpathsampling/pull/929#event-3811104273
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Sep 27, 2020 https://github.com/openpathsampling/openpathsampling/pull/929#ref-pullrequest-709759891
Internalized snapshots; random filenames for external snapshots #933 https://github.com/openpathsampling/openpathsampling/pull/933
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
misc PR https://github.com/openpathsampling/openpathsampling/issues?q=state%3Aopen%20label%3A%22misc%20PR%22
Oct 14, 2020https://github.com/openpathsampling/openpathsampling/pull/929#event-3877252984
dwhswensonhttps://github.com/dwhswenson
October 20, 2020 16:32https://github.com/openpathsampling/openpathsampling/pull/929#commits-pushed-6430927
https://github.com/dwhswenson
Merge remote-tracking branch 'upstream/master' into storable_functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/64309274c379adecb29dee9101a6ff929e00e5bb
6430927https://github.com/openpathsampling/openpathsampling/pull/929/commits/64309274c379adecb29dee9101a6ff929e00e5bb
https://github.com/dwhswenson
fix existing storage loadinghttps://github.com/openpathsampling/openpathsampling/pull/929/commits/723e8bfcb32f40a8bda9fb8175d80ba038d2c8a4
723e8bfhttps://github.com/openpathsampling/openpathsampling/pull/929/commits/723e8bfcb32f40a8bda9fb8175d80ba038d2c8a4
https://github.com/dwhswenson
add SnapshotsTable class (and tests)https://github.com/openpathsampling/openpathsampling/pull/929/commits/67177a117de98f33fed01387a035d13102ff2b79
67177a1https://github.com/openpathsampling/openpathsampling/pull/929/commits/67177a117de98f33fed01387a035d13102ff2b79
https://github.com/dwhswenson
integrate SnapshotsTable into storagehttps://github.com/openpathsampling/openpathsampling/pull/929/commits/e32c198a9d70bb53e85d21d49350d4603c53048a
e32c198https://github.com/openpathsampling/openpathsampling/pull/929/commits/e32c198a9d70bb53e85d21d49350d4603c53048a
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October 23, 2020 16:03https://github.com/openpathsampling/openpathsampling/pull/929#event-3914650408
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dwhswensonhttps://github.com/dwhswenson
Oct 24, 2020 https://github.com/openpathsampling/openpathsampling/pull/929#ref-pullrequest-727983360
SimStore Support openpathsampling/openpathsampling-cli#29 https://github.com/openpathsampling/openpathsampling-cli/pull/29
dwhswensonhttps://github.com/dwhswenson
October 24, 2020 08:05https://github.com/openpathsampling/openpathsampling/pull/929#commits-pushed-7e3a5be
https://github.com/dwhswenson
fix error in finding UUIDs in no-caching modehttps://github.com/openpathsampling/openpathsampling/pull/929/commits/7e3a5be64d7cfe0e7b26de3a245ee997537b3e8a
7e3a5behttps://github.com/openpathsampling/openpathsampling/pull/929/commits/7e3a5be64d7cfe0e7b26de3a245ee997537b3e8a
https://github.com/dwhswenson
Merge remote-tracking branch 'upstream/master' into storable_functionshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/08564c126603eb4b1e84a3c95eaf65733900193d
08564c1https://github.com/openpathsampling/openpathsampling/pull/929/commits/08564c126603eb4b1e84a3c95eaf65733900193d
https://github.com/dwhswenson
add simstore support to interface setshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/14d991389c57b798981f5a69f4cd1a6f34af4026
14d9913https://github.com/openpathsampling/openpathsampling/pull/929/commits/14d991389c57b798981f5a69f4cd1a6f34af4026
https://github.com/dwhswenson
fixes for correctly recreating nameshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/8dac4c5e1fdb9052db589b4b8d240df4ce199551
8dac4c5https://github.com/openpathsampling/openpathsampling/pull/929/commits/8dac4c5e1fdb9052db589b4b8d240df4ce199551
https://github.com/dwhswenson
better treatment of problems with name paramshttps://github.com/openpathsampling/openpathsampling/pull/929/commits/b3de2522f1ef85d2da6b637797589a2cc25d593c
b3de252https://github.com/openpathsampling/openpathsampling/pull/929/commits/b3de2522f1ef85d2da6b637797589a2cc25d593c
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Oct 24, 2020https://github.com/openpathsampling/openpathsampling/pull/929#issuecomment-715904218
dwhswenson/ops-storage-notebooks#5https://github.com/dwhswenson/ops-storage-notebooks/pull/5
Please reload this pagehttps://github.com/openpathsampling/openpathsampling/pull/929
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86eafe2https://github.com/openpathsampling/openpathsampling/commit/86eafe249e3252dbc8d6561b9988b562eed2c5a1
Oct 31, 2020https://github.com/openpathsampling/openpathsampling/pull/929#event-3944083012
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dwhswensonhttps://github.com/dwhswenson
October 31, 2020 12:44https://github.com/openpathsampling/openpathsampling/pull/929#event-3944083073
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dwhswensonhttps://github.com/dwhswenson
Oct 31, 2020 https://github.com/openpathsampling/openpathsampling/pull/929#ref-pullrequest-733712623
SimStore: Tags #940 https://github.com/openpathsampling/openpathsampling/pull/940
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dwhswensonhttps://github.com/dwhswenson
Dec 23, 2020 https://github.com/openpathsampling/openpathsampling/pull/929#ref-pullrequest-773555507
Release 1.4.0 #952 https://github.com/openpathsampling/openpathsampling/pull/952
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