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Round minutes in StdOutLogger; add forcefield pickle method to System, fix write mode in to_gsd, add flush_writers method and add parameter for max buffer size. #85

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merged 11 commits into from
Oct 31, 2023
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Round minutes in StdOutLogger; add forcefield pickle method to System, fix write mode in to_gsd, add flush_writers method and add parameter for max buffer size. #85

merged 11 commits into from
Oct 31, 2023

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chrisjonesBSU
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This PR addresses each of the bug/issues in #78

@chrisjonesBSU chrisjonesBSU linked an issue Oct 30, 2023 that may be closed by this pull request
Minor bugs/features #78
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codecov bot commented Oct 30, 2023 •
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Codecov Report

Merging #85 (8d112ae) into main (018fb9e) will increase coverage by 0.05%.
Report is 2 commits behind head on main.
The diff coverage is 86.66%.

Additional details and impacted files

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@@            Coverage Diff             @@
##             main      #85      +/-   ##
==========================================
+ Coverage   93.81%   93.86%   +0.05%     
==========================================
  Files          20       20              
  Lines        1535     1549      +14     
==========================================
+ Hits         1440     1454      +14     
  Misses         95       95
Files Coverage Δ
flowermd/base/simulation.py 91.44% <100.00%> (+0.15%) ⬆️
flowermd/base/system.py 91.51% <100.00%> (+0.90%) ⬆️
flowermd/utils/actions.py 84.90% <0.00%> (-3.33%) ⬇️

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I also added a parameter to set the maximum buffer size before writing to file, and a method that can flush all writers that use a buffer. This addresses #59

@chrisjonesBSU chrisjonesBSU linked an issue Oct 30, 2023 that may be closed by this pull request
Set GSD writer buffer size #59
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@chrisjonesBSU chrisjonesBSU changed the title Round minutes in StdOutLogger; add forcefield pickle method to System, fix write mode in to_gsd Round minutes in StdOutLogger; add forcefield pickle method to System, fix write mode in to_gsd, add flush_writers method and add parameter for max buffer size. Oct 30, 2023
marjanalbooyeh
marjanalbooyeh approved these changes Oct 31, 2023
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LGTM, just left a comment.
Thanks for taking care of these bugs Chris!

flowermd/tests/base/test_simulation.py Outdated Show resolved Hide resolved
@chrisjonesBSU chrisjonesBSU merged commit 83d31d9 into cmelab:main Oct 31, 2023
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@chrisjonesBSU chrisjonesBSU deleted the round_eta branch October 31, 2023 17:04
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@marjanalbooyeh marjanalbooyeh marjanalbooyeh approved these changes

@RainierBarrett RainierBarrett Awaiting requested review from RainierBarrett

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Successfully merging this pull request may close these issues.

Minor bugs/features Set GSD writer buffer size
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@chrisjonesBSU @marjanalbooyeh