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Title: `compile` command: Simulation setup with YAML or JSON by dwhswenson · Pull Request #43 · openpathsampling/openpathsampling-cli · GitHub

Open Graph Title: `compile` command: Simulation setup with YAML or JSON by dwhswenson · Pull Request #43 · openpathsampling/openpathsampling-cli

X Title: `compile` command: Simulation setup with YAML or JSON by dwhswenson · Pull Request #43 · openpathsampling/openpathsampling-cli

Description: This PR adds tools to parse YAML files for simulation setup. This allows for a yaml -> .db translation in a new command called compile. This builds on #41 and should only be merged after that.

Open Graph Description: This PR adds tools to parse YAML files for simulation setup. This allows for a yaml -> .db translation in a new command called compile. This builds on #41 and should only be merged after that.

X Description: This PR adds tools to parse YAML files for simulation setup. This allows for a yaml -> .db translation in a new command called compile. This builds on #41 and should only be merged after that.

Opengraph URL: https://github.com/openpathsampling/openpathsampling-cli/pull/43

X: @github

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Domain: github.com

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compile command: Simulation setup with YAML or JSON https://github.com/openpathsampling/openpathsampling-cli/pull/43#top
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Add core & engines for yaml compilinghttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/1850972803c55db40a3ea0c7a9a77aa7bfcee1ad
1850972https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/1850972803c55db40a3ea0c7a9a77aa7bfcee1ad
https://github.com/dwhswenson
Remove named_obj param in engines, topologieshttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/4392e41374edd177036a49887616d6e54d6d5c3a
4392e41https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/4392e41374edd177036a49887616d6e54d6d5c3a
https://github.com/dwhswenson
CVs and tests (without named_objs)https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/2a81273180d4f67ac7fdaec2ed5bd19a26f849ba
2a81273https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/2a81273180d4f67ac7fdaec2ed5bd19a26f849ba
https://github.com/dwhswenson
volumes and partial tests for volumeshttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/3be9450d7616e9a08f944ea245e691ecee85f9ab
3be9450https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/3be9450d7616e9a08f944ea245e691ecee85f9ab
https://github.com/dwhswenson
Moved tests over to testing dirhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/dfbf36cb86bd935452903f2cdece51ddd84100ec
dfbf36chttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/dfbf36cb86bd935452903f2cdece51ddd84100ec
https://github.com/dwhswenson
remove named objs; still seems to workhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/e1a778f771651a91df5c8051dc882f2634f7dcb4
e1a778fhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/e1a778f771651a91df5c8051dc882f2634f7dcb4
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Seems to work up to networks now!https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/b3edf0409b28dda4a27882090923743a2128604e
b3edf04https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/b3edf0409b28dda4a27882090923743a2128604e
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Seems to work through TPS schemes!https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/2ed6990de1b29529bc526b4671abfe597550d32e
2ed6990https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/2ed6990de1b29529bc526b4671abfe597550d32e
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steps toward parsing simulationshttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/3c45b8724852def65ddd75ce671179466f0d77d3
3c45b87https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/3c45b8724852def65ddd75ce671179466f0d77d3
https://github.com/dwhswenson
Add compile commandhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/248cef061f510f2922e58655a2fedceed17b985a
248cef0https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/248cef061f510f2922e58655a2fedceed17b985a
https://github.com/dwhswenson
Merge branch 'main' into sim-setuphttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/10ce9d2114a68f1d03111db0b02658a3b385766b
10ce9d2https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/10ce9d2114a68f1d03111db0b02658a3b385766b
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enhancement https://github.com/openpathsampling/openpathsampling-cli/issues?q=state%3Aopen%20label%3Aenhancement
Apr 18, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/43#event-4609299055
https://github.com/dwhswenson
Merge branch 'wizard' into sim-setuphttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/0657882cb42b7d67a2043d12cb2fbcea1fb13daf
0657882https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/0657882cb42b7d67a2043d12cb2fbcea1fb13daf
https://github.com/dwhswenson
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Jul 24, 2021 https://github.com/openpathsampling/openpathsampling-cli/pull/43#ref-pullrequest-822305440
Simulation Setup Wizard #41 https://github.com/openpathsampling/openpathsampling-cli/pull/41
dwhswensonhttps://github.com/dwhswenson
July 24, 2021 10:31https://github.com/openpathsampling/openpathsampling-cli/pull/43#commits-pushed-45e77d6
https://github.com/dwhswenson
long forgotten stash with lots of useful stuffhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/45e77d682e9ee77aba8eb9622d037c71984a9c79
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add tests/parsing/__init__.pyhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/728083c96892b6f0628205c8abb5b8381f89f0a4
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tests for volumes combinationshttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/87029ddd8fc7db8e50f43051ae13f572079c02c4
87029ddhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/87029ddd8fc7db8e50f43051ae13f572079c02c4
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fix for location of MDTrajTopologyhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/ef1f08611768dd09aaba5db7fcbed98751c5cdd9
ef1f086https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/ef1f08611768dd09aaba5db7fcbed98751c5cdd9
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improvements to testinghttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/55c2dbd38f39a7f8d35dc7f59ce398d258599df1
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fix name of unit when Nonehttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/2dad4d81a54c49a49ddc47aff31cdb88df63af92
2dad4d8https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/2dad4d81a54c49a49ddc47aff31cdb88df63af92
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fix skiptesthttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/0b106e6b06b0d9be003d46c40e6bbf2dbc7d857a
0b106e6https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/0b106e6b06b0d9be003d46c40e6bbf2dbc7d857a
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use custom_eval_int_strict_poshttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/ff4bc7806406ba31cb6e6b67d859e0e17d14f3e9
ff4bc78https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/ff4bc7806406ba31cb6e6b67d859e0e17d14f3e9
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bring coverage back to 100%https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/63a0f337684c01f882308db2f01fb2cc6f37713e
63a0f33https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/63a0f337684c01f882308db2f01fb2cc6f37713e
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don't use endswith on possible Nonehttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/3fd2509c19895f807c2c202cf84b400134643964
3fd2509https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/3fd2509c19895f807c2c202cf84b400134643964
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Sep 26, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/43#issuecomment-927346120
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View reviewed changes https://github.com/openpathsampling/openpathsampling-cli/pull/43/files/3fd2509c19895f807c2c202cf84b400134643964
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paths_cli/compiling/core.pyhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/files/3fd2509c19895f807c2c202cf84b400134643964#diff-afaba9c02bc335ef7c40b8a5ac97c6b0c8a6fedbe0d8fa76466255e464e8e333
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paths_cli/compiling/engines.pyhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/files/3fd2509c19895f807c2c202cf84b400134643964#diff-6740987de3367ec1593341362c6d3d233142112d4b9b8e4a31be242550a894cf
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paths_cli/tests/compiling/test_tools.pyhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/files/3fd2509c19895f807c2c202cf84b400134643964#diff-971706656c081fb32957ad265a7e33426548face90400d00871d82cb8eeddb23
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September 27, 2021 12:27https://github.com/openpathsampling/openpathsampling-cli/pull/43#commits-pushed-854137c
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cleanup per review commentshttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/854137c2beb886dbe7c7c7cd16e1d32bff666a41
854137chttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/854137c2beb886dbe7c7c7cd16e1d32bff666a41
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Update paths_cli/compiling/core.pyhttps://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/a43b2c003bcf50aea6c0ac0d2938dc72a5c35ab7
a43b2c0https://github.com/openpathsampling/openpathsampling-cli/pull/43/commits/a43b2c003bcf50aea6c0ac0d2938dc72a5c35ab7
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Sep 27, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/43#issuecomment-928060205
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8f6a797https://github.com/openpathsampling/openpathsampling-cli/commit/8f6a79789ca6dfd6204953ed314a0c1afdbc03ae
Sep 27, 2021https://github.com/openpathsampling/openpathsampling-cli/pull/43#event-5366961177
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September 27, 2021 16:43https://github.com/openpathsampling/openpathsampling-cli/pull/43#event-5366961514
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Oct 7, 2021 https://github.com/openpathsampling/openpathsampling-cli/pull/43#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/43#ref-pullrequest-2345239648
Release 0.3 #79 https://github.com/openpathsampling/openpathsampling-cli/pull/79
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