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Title: Simulation Setup Wizard by dwhswenson · Pull Request #41 · openpathsampling/openpathsampling-cli · GitHub

Open Graph Title: Simulation Setup Wizard by dwhswenson · Pull Request #41 · openpathsampling/openpathsampling-cli

X Title: Simulation Setup Wizard by dwhswenson · Pull Request #41 · openpathsampling/openpathsampling-cli

Description: This will add an interactive setup wizard to the OPS CLI. The wizard will guide users through the process of setting up simulation objects to use in a simulation, and will save the created objects ...

Open Graph Description: This will add an interactive setup wizard to the OPS CLI. The wizard will guide users through the process of setting up simulation objects to use in a simulation, and will save the created objects ...

X Description: This will add an interactive setup wizard to the OPS CLI. The wizard will guide users through the process of setting up simulation objects to use in a simulation, and will save the created objects ...

Opengraph URL: https://github.com/openpathsampling/openpathsampling-cli/pull/41

X: @github

direct link

Domain: github.com

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og:image:altThis will add an interactive setup wizard to the OPS CLI. The wizard will guide users through the process of setting up simulation objects to use in a simulation, and will save the created objects ...
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openpathsampling:mainhttps://github.com/openpathsampling/openpathsampling-cli/tree/main
dwhswenson:wizardhttps://github.com/dwhswenson/openpathsampling-cli/tree/wizard
Simulation Setup Wizard https://github.com/openpathsampling/openpathsampling-cli/pull/41#top
dwhswensonhttps://github.com/dwhswenson
openpathsampling:mainhttps://github.com/openpathsampling/openpathsampling-cli/tree/main
dwhswenson:wizardhttps://github.com/dwhswenson/openpathsampling-cli/tree/wizard
Conversation 42 https://github.com/openpathsampling/openpathsampling-cli/pull/41
Commits 49 https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits
Checks 0 https://github.com/openpathsampling/openpathsampling-cli/pull/41/checks
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Mar 4, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/41#issue-822305440
Please reload this pagehttps://github.com/openpathsampling/openpathsampling-cli/pull/41
dwhswensonhttps://github.com/dwhswenson
February 18, 2021 09:27https://github.com/openpathsampling/openpathsampling-cli/pull/41#commits-pushed-7af7eae
https://github.com/dwhswenson
Add start to wizardhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/7af7eae0c92986ef1f90fe31f94cc72690a20e1e
7af7eaehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/7af7eae0c92986ef1f90fe31f94cc72690a20e1e
https://github.com/dwhswenson
TPS wizard works through state defshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/7fec89197f8284d9dfcd66b4f001cbbd7c52e80e
7fec891https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/7fec89197f8284d9dfcd66b4f001cbbd7c52e80e
https://github.com/dwhswenson
a little more work on the wizardhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/250f4e27563b5916d59d1ac605629ad5be29a644
250f4e2https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/250f4e27563b5916d59d1ac605629ad5be29a644
https://github.com/dwhswenson
major steps toward TPS wizardhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/666f9a997edbedabf302fde34e59eebe3f41168b
666f9a9https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/666f9a997edbedabf302fde34e59eebe3f41168b
https://github.com/dwhswenson
A little more cleanup on wizard stuffhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/8910ba22e68e35a4ab6f0dbeb6a4810d0543b9d8
8910ba2https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/8910ba22e68e35a4ab6f0dbeb6a4810d0543b9d8
https://github.com/dwhswenson
Start to add tests for wizardhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/0b60338d67114507c54f0dd0596f7dcd507d059b
0b60338https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/0b60338d67114507c54f0dd0596f7dcd507d059b
https://github.com/dwhswenson
tests for most of the Wizard objecthttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/68066b1477356874b4c2b398dfe6751c66c8ec2b
68066b1https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/68066b1477356874b4c2b398dfe6751c66c8ec2b
https://github.com/dwhswenson
move MockConsole, start to get_object decoratorhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/4da1b9a2f34bd5dffb96ca2cec94019f8bcbc520
4da1b9ahttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/4da1b9a2f34bd5dffb96ca2cec94019f8bcbc520
https://github.com/dwhswenson
more work toward using get_objecthttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/c17f3d1d44c23a77011cb55a1a855213326e8c7b
c17f3d1https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/c17f3d1d44c23a77011cb55a1a855213326e8c7b
https://github.com/dwhswenson
tests for OpenMM wizardhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/77fa5cec7c3952a292796c365663674dfea521a2
77fa5cehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/77fa5cec7c3952a292796c365663674dfea521a2
https://github.com/dwhswenson
Prep tests for CVshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/76ea517b5e113832d34d1fa51718786a39e81394
76ea517https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/76ea517b5e113832d34d1fa51718786a39e81394
https://github.com/dwhswenson
Some CV cleanup; more periodicity to CVshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/5d2e3f86e818220e2b581a38a4e8bb2409f3d533
5d2e3f8https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/5d2e3f86e818220e2b581a38a4e8bb2409f3d533
https://github.com/dwhswenson
Wizard ready for 2-state TPS demohttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/b5ec9ce5742ee8682e4b2ce0707e7888b9d2ccbe
b5ec9cehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/b5ec9ce5742ee8682e4b2ce0707e7888b9d2ccbe
https://github.com/dwhswenson
Add tests for CV wizardshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/b32d03a1767a792d390d0db44f5b42d2644ec21e
b32d03ahttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/b32d03a1767a792d390d0db44f5b42d2644ec21e
https://github.com/dwhswenson
tests for volume wizardshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/a52bac0b3aaf9773638f26f2359c28a7e7efe554
a52bac0https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/a52bac0b3aaf9773638f26f2359c28a7e7efe554
https://github.com/dwhswenson
simplify code to reflect current usagehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/a9c4d960ff325c1d3878b94a7ddcb68b143a5b56
a9c4d96https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/a9c4d960ff325c1d3878b94a7ddcb68b143a5b56
https://github.com/dwhswenson
more cleanup of unusedhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/a85118fd5544a79d93d3b2176815a4db798c5494
a85118fhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/a85118fd5544a79d93d3b2176815a4db798c5494
https://github.com/dwhswenson
More tests; work toward handling Spring Shootinghttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/42aa3c9c9e47e1bb4f65d541daeddb7f4028eb85
42aa3c9https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/42aa3c9c9e47e1bb4f65d541daeddb7f4028eb85
https://github.com/dwhswenson
fix up testshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/13f7108f688d1dcb7d1d8df399e92f0ad8730f93
13f7108https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/13f7108f688d1dcb7d1d8df399e92f0ad8730f93
https://github.com/dwhswenson
Add tests for shooting, load_from_opshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/9d6c3dda089d6b5c5caf515fb08d12f6ca425236
9d6c3ddhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/9d6c3dda089d6b5c5caf515fb08d12f6ca425236
https://github.com/dwhswenson
Remove name from core (used as wizard.name)https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/6467b59721d07d2b5ae6e4346fe41e5dbd5c75a1
6467b59https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/6467b59721d07d2b5ae6e4346fe41e5dbd5c75a1
https://github.com/dwhswenson
Add tests for TPS wizardhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/d2050e4ab4cf946254b3dda3fe5efca86110c2ab
d2050e4https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/d2050e4ab4cf946254b3dda3fe5efca86110c2ab
https://github.com/dwhswenson
Tests for two_state_tps.pyhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/94cd34e80c6b7cf7b53dc0016b0017d7fefbccb0
94cd34ehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/94cd34e80c6b7cf7b53dc0016b0017d7fefbccb0
https://github.com/dwhswenson
tests for engines and errorshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/3f183de908cfcf8afb78ac456832d7e1b9e45c9b
3f183dehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/3f183de908cfcf8afb78ac456832d7e1b9e45c9b
https://github.com/dwhswenson
Update for parsing.tools.custom_evalhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/35c9ca18ce330b6871e8d3b01d7c8e77266bdf1b
35c9ca1https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/35c9ca18ce330b6871e8d3b01d7c8e77266bdf1b
https://github.com/dwhswenson
split off _do_one in wizardhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/97189a6ac0eacd607da36bdc6d4ba89853552ee5
97189a6https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/97189a6ac0eacd607da36bdc6d4ba89853552ee5
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
enhancement https://github.com/openpathsampling/openpathsampling-cli/issues?q=state%3Aopen%20label%3Aenhancement
Apr 9, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/41#event-4575249519
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Apr 18, 2021 https://github.com/openpathsampling/openpathsampling-cli/pull/41#ref-pullrequest-860712769
compile command: Simulation setup with YAML or JSON #43 https://github.com/openpathsampling/openpathsampling-cli/pull/43
https://github.com/dwhswenson
Add remaining tests for wizardhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/f932fce870236522fdb0cb5920f0fe0681f57d2e
f932fcehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/f932fce870236522fdb0cb5920f0fe0681f57d2e
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Jun 18, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/41#event-4911433510
https://github.com/dwhswenson
don't actually monkeypatch when testing Wizardhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/6c37dce94df2305c74bd6c05a26b3b2d745cf4e1
6c37dcehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/6c37dce94df2305c74bd6c05a26b3b2d745cf4e1
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Jun 18, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/41#issuecomment-864293906
Please reload this pagehttps://github.com/openpathsampling/openpathsampling-cli/pull/41
https://github.com/dwhswenson
fix deprecation warnings for OPS 1.5https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/d444895b81fb7a67196fe7e9e4db8cb36860c77c
d444895https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/d444895b81fb7a67196fe7e9e4db8cb36860c77c
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Jul 6, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/41#issuecomment-875078746
Please reload this pagehttps://github.com/openpathsampling/openpathsampling-cli/pull/41
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Jul 6, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/41#event-4985495911
https://github.com/dwhswenson
dwhswensonhttps://github.com/dwhswenson
Jul 6, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/41#event-4985496181
dwhswensonhttps://github.com/dwhswenson
July 7, 2021 03:37https://github.com/openpathsampling/openpathsampling-cli/pull/41#commits-pushed-47106e6
https://github.com/dwhswenson
Add Wizard (skeleton form) to docshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/47106e6ef599bec29eaec25957c6d06ac0134d98
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Add test job with openmm etc integrationshttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/e9dd8158f4d93d7152fb0ae6925a34acbcfe2ced
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fix whitespace in yamlhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/ea29ac49c902cdb764d6ef5ab64ce68f53f9539a
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fix include in yamlhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/b52c1efaa9a8e4b255b6120d958152601d6866f6
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fix typo in workflowhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/3b64ce7112d6cf871731a5a1cbad8fd76684f9c5
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fix workflowhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/8dcd07d3484da34c30ad01bbb520ea65be46663e
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increase fetch-depth to help codecovhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/e774caace4e91d9724e0b95cc6eeb6e4976525c7
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... helps is fetch-depth is in the right headinghttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/d07699ea9590312646e003ae4d7cfac9a800dcef
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finish test coveragehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/2ba6390a446c80835d027e6bac4bc8b8129e308a
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Add test for bad MDTraj atom index inputhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/59b6fbed0153e395b74f44a8d708319e18c95aae
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Add tests/wizard/__init__.pyhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/4f3e53aa2032efd5f4b8138776f1d032123b89e5
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no-cov on jokehttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/0b33b7938520138549892d6ab7989694c23ccb7e
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July 26, 2021 13:25https://github.com/openpathsampling/openpathsampling-cli/pull/41#commits-pushed-60eb119
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Apply suggestions from code reviewhttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/60eb119540e39642daa0313cc09b5ca507d8767b
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misc review cleanuphttps://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/3d92cd248060aac02acc0e9686408ef914e2d62b
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Merge branch 'main' of github.com:openpathsampling/openpathsampling-c…https://github.com/openpathsampling/openpathsampling-cli/pull/41/commits/07b7d7cb2e25fa81c4ff68adb1ae779b17d47842
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Jul 27, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/41#issuecomment-887699479
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Jul 27, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/41#event-5075727248
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July 27, 2021 17:33https://github.com/openpathsampling/openpathsampling-cli/pull/41#event-5075727468
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Sep 2, 2021 https://github.com/openpathsampling/openpathsampling-cli/pull/41#ref-pullrequest-985878935
Updates for OpenMM 7.6 #50 https://github.com/openpathsampling/openpathsampling-cli/pull/50
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Oct 7, 2021 https://github.com/openpathsampling/openpathsampling-cli/pull/41#ref-pullrequest-1019523706
Wizard rewrite #54 https://github.com/openpathsampling/openpathsampling-cli/pull/54
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Jun 11, 2024 https://github.com/openpathsampling/openpathsampling-cli/pull/41#ref-pullrequest-2345239648
Release 0.3 #79 https://github.com/openpathsampling/openpathsampling-cli/pull/79
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