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Title: SimStore: New storage subsystem (part 1) by dwhswenson · Pull Request #928 · openpathsampling/openpathsampling · GitHub

Open Graph Title: SimStore: New storage subsystem (part 1) by dwhswenson · Pull Request #928 · openpathsampling/openpathsampling

X Title: SimStore: New storage subsystem (part 1) by dwhswenson · Pull Request #928 · openpathsampling/openpathsampling

Description: For a while, I've been trying to rework our storage. This is because of several problems with the netcdfplus package: It doesn't seem to play nicely with dask, which I intend to use for paralleliz...

Open Graph Description: For a while, I've been trying to rework our storage. This is because of several problems with the netcdfplus package: It doesn't seem to play nicely with dask, which I intend to use for pa...

X Description: For a while, I've been trying to rework our storage. This is because of several problems with the netcdfplus package: It doesn't seem to play nicely with dask, which I intend to us...

Opengraph URL: https://github.com/openpathsampling/openpathsampling/pull/928

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dwhswenson:storagehttps://github.com/dwhswenson/openpathsampling/tree/storage
SimStore: New storage subsystem (part 1) https://github.com/openpathsampling/openpathsampling/pull/928#top
dwhswensonhttps://github.com/dwhswenson
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dwhswenson:storagehttps://github.com/dwhswenson/openpathsampling/tree/storage
Conversation 21 https://github.com/openpathsampling/openpathsampling/pull/928
Commits 176 https://github.com/openpathsampling/openpathsampling/pull/928/commits
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Sep 17, 2020https://github.com/openpathsampling/openpathsampling/pull/928#issue-703682052
daskhttp://dask.pydata.org/
@jhprinzhttps://github.com/jhprinz
https://github.com/dwhswenson/ops-storage-notebookshttps://github.com/dwhswenson/ops-storage-notebooks
Please reload this pagehttps://github.com/openpathsampling/openpathsampling/pull/928
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January 31, 2018 19:45https://github.com/openpathsampling/openpathsampling/pull/928#commits-pushed-2f072da
https://github.com/dwhswenson
Start to sql-based storagehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/2f072dad56a362f1b2d31e40065bf0466be96930
2f072dahttps://github.com/openpathsampling/openpathsampling/pull/928/commits/2f072dad56a362f1b2d31e40065bf0466be96930
https://github.com/dwhswenson
more tests for sql-based storagehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/c320ba4d7bd8e3908a0ce7e5657b53e84bfc20ca
c320ba4https://github.com/openpathsampling/openpathsampling/pull/928/commits/c320ba4d7bd8e3908a0ce7e5657b53e84bfc20ca
https://github.com/dwhswenson
Another test for new storagehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/5d40746151cca979d90914226fc68c7b68ecee76
5d40746https://github.com/openpathsampling/openpathsampling/pull/928/commits/5d40746151cca979d90914226fc68c7b68ecee76
https://github.com/dwhswenson
progress on sql backendhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/a4ef3b9b4810d4dd8f6cd5cfe00d8b5d9312582b
a4ef3b9https://github.com/openpathsampling/openpathsampling/pull/928/commits/a4ef3b9b4810d4dd8f6cd5cfe00d8b5d9312582b
https://github.com/dwhswenson
move file nameshttps://github.com/openpathsampling/openpathsampling/pull/928/commits/968219b42266f6b9344045061ddaca1757d73f8a
968219bhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/968219b42266f6b9344045061ddaca1757d73f8a
https://github.com/dwhswenson
Split off storage from sql_backendhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/14659cf5b72c5aa12aa085357948437b14d65356
14659cfhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/14659cf5b72c5aa12aa085357948437b14d65356
https://github.com/dwhswenson
fix up testshttps://github.com/openpathsampling/openpathsampling/pull/928/commits/9197ae1f0db39f360ad1695bc311b0f4874acf59
9197ae1https://github.com/openpathsampling/openpathsampling/pull/928/commits/9197ae1f0db39f360ad1695bc311b0f4874acf59
https://github.com/dwhswenson
add_to_table seems to be workinghttps://github.com/openpathsampling/openpathsampling/pull/928/commits/298ce49064d9fe3cc45d4cf44fd895d47e5e8e9e
298ce49https://github.com/openpathsampling/openpathsampling/pull/928/commits/298ce49064d9fe3cc45d4cf44fd895d47e5e8e9e
https://github.com/dwhswenson
more drafts of loading function for sql storagehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/23f0f7b6e96f0d434e832bda7a741be2c10faf8a
23f0f7bhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/23f0f7b6e96f0d434e832bda7a741be2c10faf8a
https://github.com/dwhswenson
always use UUID columnshttps://github.com/openpathsampling/openpathsampling/pull/928/commits/f4809848b675294ed81e492871b21a301a44e1fb
f480984https://github.com/openpathsampling/openpathsampling/pull/928/commits/f4809848b675294ed81e492871b21a301a44e1fb
https://github.com/dwhswenson
test int_table_from_db; smoketest load_uuidshttps://github.com/openpathsampling/openpathsampling/pull/928/commits/cfaf730aec2fa91a1feb0d3ab16d254f4cde7e76
cfaf730https://github.com/openpathsampling/openpathsampling/pull/928/commits/cfaf730aec2fa91a1feb0d3ab16d254f4cde7e76
https://github.com/dwhswenson
full test for add_to_tablehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/5fefb55331dccde843fe0bf3044f38468b9ea2bb
5fefb55https://github.com/openpathsampling/openpathsampling/pull/928/commits/5fefb55331dccde843fe0bf3044f38468b9ea2bb
https://github.com/dwhswenson
more steps on storagehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/97ec6c825459f57bae23c66a9d3ebbe805dd912b
97ec6c8https://github.com/openpathsampling/openpathsampling/pull/928/commits/97ec6c825459f57bae23c66a9d3ebbe805dd912b
https://github.com/dwhswenson
Merge branch 'typecheck_unicode_is_str' into storagehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/669a4333f1ce32e6a07ce418eb357d1e73909b27
669a433https://github.com/openpathsampling/openpathsampling/pull/928/commits/669a4333f1ce32e6a07ce418eb357d1e73909b27
https://github.com/dwhswenson
Added most of serializationhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/4b0894caf19e412c81ea2b4aa8588d90caef6aca
4b0894chttps://github.com/openpathsampling/openpathsampling/pull/928/commits/4b0894caf19e412c81ea2b4aa8588d90caef6aca
https://github.com/dwhswenson
Merge remote-tracking branch 'upstream/master' into storagehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/b5fbda14a4d1af963df2ce453c0b00a1a07ce17b
b5fbda1https://github.com/openpathsampling/openpathsampling/pull/928/commits/b5fbda14a4d1af963df2ce453c0b00a1a07ce17b
https://github.com/dwhswenson
start thinking about lazy loadinghttps://github.com/openpathsampling/openpathsampling/pull/928/commits/dd4613d6b6b49aee2886818a9b7fde5653c7b23d
dd4613dhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/dd4613d6b6b49aee2886818a9b7fde5653c7b23d
https://github.com/dwhswenson
added draft of OPS schemahttps://github.com/openpathsampling/openpathsampling/pull/928/commits/48f3f6078148c278d49219afd923d6c5c70ebcd4
48f3f60https://github.com/openpathsampling/openpathsampling/pull/928/commits/48f3f6078148c278d49219afd923d6c5c70ebcd4
https://github.com/dwhswenson
work on tests for sql_backendhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/84a073ea1e0ab6144c85bd5e3a1acad28e2703cd
84a073ehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/84a073ea1e0ab6144c85bd5e3a1acad28e2703cd
https://github.com/dwhswenson
tests for some of the tools methodshttps://github.com/openpathsampling/openpathsampling/pull/928/commits/01a635f5da47f0524af8ae8f0aefb3d8c5c57cc2
01a635fhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/01a635f5da47f0524af8ae8f0aefb3d8c5c57cc2
https://github.com/dwhswenson
majot work on save methodhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/ea56dad07ac214e8ba0c380ceff5e935d1d9d998
ea56dadhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/ea56dad07ac214e8ba0c380ceff5e935d1d9d998
https://github.com/dwhswenson
reorg for more straightforward setuphttps://github.com/openpathsampling/openpathsampling/pull/928/commits/f6c75f8c61ded76d9d0267e82dbd52a11c1e93d3
f6c75f8https://github.com/openpathsampling/openpathsampling/pull/928/commits/f6c75f8c61ded76d9d0267e82dbd52a11c1e93d3
https://github.com/dwhswenson
steps toward serializationhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/06b2e78140a3d55b2a4a6a013dacf80d34393c42
06b2e78https://github.com/openpathsampling/openpathsampling/pull/928/commits/06b2e78140a3d55b2a4a6a013dacf80d34393c42
https://github.com/dwhswenson
successful storing of a PES with storage.save()https://github.com/openpathsampling/openpathsampling/pull/928/commits/af2ce7655a0ae8d868764e4fc8c54005ad7c3bb9
af2ce76https://github.com/openpathsampling/openpathsampling/pull/928/commits/af2ce7655a0ae8d868764e4fc8c54005ad7c3bb9
https://github.com/dwhswenson
starting on numpy supporthttps://github.com/openpathsampling/openpathsampling/pull/928/commits/573c554e8d90b9fbef9d39506d60eec58c61bdb6
573c554https://github.com/openpathsampling/openpathsampling/pull/928/commits/573c554e8d90b9fbef9d39506d60eec58c61bdb6
https://github.com/dwhswenson
fix testshttps://github.com/openpathsampling/openpathsampling/pull/928/commits/1767b4f413a2b0ff26a3334183833c4e561ddc6f
1767b4fhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/1767b4f413a2b0ff26a3334183833c4e561ddc6f
https://github.com/dwhswenson
progress on numpy supporthttps://github.com/openpathsampling/openpathsampling/pull/928/commits/754ff2019127c25885cb5cb090ea6b246fb396bf
754ff20https://github.com/openpathsampling/openpathsampling/pull/928/commits/754ff2019127c25885cb5cb090ea6b246fb396bf
https://github.com/dwhswenson
numpy can be serialized/deserializedhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/e3858f9379d43c5ae56e7c48b7a5fddad148f32a
e3858f9https://github.com/openpathsampling/openpathsampling/pull/928/commits/e3858f9379d43c5ae56e7c48b7a5fddad148f32a
https://github.com/dwhswenson
save snapshots and sim objshttps://github.com/openpathsampling/openpathsampling/pull/928/commits/3ca393d7959ba9b4b32f62a65897a8e454067d2b
3ca393dhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/3ca393d7959ba9b4b32f62a65897a8e454067d2b
https://github.com/dwhswenson
Snapshots fully save with manual registrationhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/0fbf74ea1be32fdca3c879437e3aed78e6c01055
0fbf74ehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/0fbf74ea1be32fdca3c879437e3aed78e6c01055
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Sep 24, 2020https://github.com/openpathsampling/openpathsampling/pull/928#issuecomment-698280723
@sroethttps://github.com/sroet
Please reload this pagehttps://github.com/openpathsampling/openpathsampling/pull/928
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sroethttps://github.com/sroet
Sep 24, 2020https://github.com/openpathsampling/openpathsampling/pull/928#issuecomment-698289650
Please reload this pagehttps://github.com/openpathsampling/openpathsampling/pull/928
Please reload this pagehttps://github.com/openpathsampling/openpathsampling/pull/928
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September 24, 2020 18:54https://github.com/openpathsampling/openpathsampling/pull/928#commits-pushed-65f71e1
https://github.com/dwhswenson
fix obvious mistakehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/65f71e160d8fdbbc96beb61ec82e2df5bd9cb499
65f71e1https://github.com/openpathsampling/openpathsampling/pull/928/commits/65f71e160d8fdbbc96beb61ec82e2df5bd9cb499
https://github.com/dwhswenson
Remove cache from StorageTable.__init__ (unused)https://github.com/openpathsampling/openpathsampling/pull/928/commits/592429edcf816534158743d2c32e364921961413
592429ehttps://github.com/openpathsampling/openpathsampling/pull/928/commits/592429edcf816534158743d2c32e364921961413
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Sep 25, 2020https://github.com/openpathsampling/openpathsampling/pull/928#issuecomment-698858955
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Sep 25, 2020 https://github.com/openpathsampling/openpathsampling/pull/928#ref-pullrequest-708853499
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build index on uuid table on creationhttps://github.com/openpathsampling/openpathsampling/pull/928/commits/a2706ccb5a70b5db2e3a4ab9719aa11e0c5a75b0
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Outside-API subpackages: experimental and beta #813 https://github.com/openpathsampling/openpathsampling/issues/813
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January 17, 2021 11:54https://github.com/openpathsampling/openpathsampling/pull/928#event-4215027431
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Use a deque to keep track of more recent time estimates #989 https://github.com/openpathsampling/openpathsampling/pull/989
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