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Gromacs Run Unit for the MD protocol #13

Merged

hannahbaumann merged 34 commits into main from gmx_run_unit

Sep 23, 2024

Contributor

hannahbaumann commented Jul 31, 2024

Description

Provide a brief description of the PR's purpose here.

Todos

Notable points that this PR has either accomplished or will accomplish.

TODO 1

Questions

Question1

Status

Ready to go


          Start Gromacs Run Unit

4ad39be

pep8speaks commented Jul 31, 2024 •

edited

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Hello @hannahbaumann! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file openfe_gromacs/protocols/gromacs_md/md_methods.py:

Line 1089:80: E501 line too long (88 > 79 characters)
Line 1090:80: E501 line too long (88 > 79 characters)
Line 1097:80: E501 line too long (83 > 79 characters)
Line 1098:80: E501 line too long (86 > 79 characters)
Line 1099:80: E501 line too long (86 > 79 characters)
Line 1178:80: E501 line too long (81 > 79 characters)
Line 1180:80: E501 line too long (80 > 79 characters)

Comment last updated at 2024-09-23 08:47:56 UTC

pre-commit-ci bot and others added 12 commits

July 31, 2024 13:59


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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          Add NVT, NPT

f9a5aea


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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          Add more output settings


          [pre-commit.ci] auto fixes from pre-commit.com hooks

0a829e8

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          return file paths for all Gromacs outputs


          some fixes

a075e4c


          Changing the tests

e8a6796


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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          Add more outputs and update tests

9f8e20d


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          small test

8f0133e

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Base automatically changed from start_GromacsMDProtocol to main

September 20, 2024 10:26

hannahbaumann and others added 8 commits

September 20, 2024 12:32


          Merge main

e19b870


          Fix style

0dce60e


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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          Change function to staticmethod

6f62512


          Merge branch 'gmx_run_unit' of github.com:OpenFreeEnergy/openfe-groma…

7c17e79

…cs into gmx_run_unit


          Add typing to _run function

714d86e


          Remove duplicate function

c9ee512


          Output files together as dict

e52a3d9

pre-commit-ci bot and others added 7 commits

September 20, 2024 12:26


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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          Update tests run units

68cc7f9


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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          Update results file

f60a884


          Small fix

df1f4b3


          Update tokenization test

9ead38a


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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codecov bot commented Sep 20, 2024 •

edited

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Codecov Report

Attention: Patch coverage is 96.82540% with 4 lines in your changes missing coverage. Please review.

Project coverage is 92.14%. Comparing base (3124bc1) to head (790cd2e).
Report is 35 commits behind head on main.

Additional details and impacted files

hannahbaumann and others added 6 commits

September 23, 2024 10:06


          Use .gro file from previous step

557c453


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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          For now add ntomp to the SimulationSettings

fe82c07


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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          Small fix

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          Update tokens

790cd2e

hannahbaumann merged commit 14ab594 into main

7 of 9 checks passed

hannahbaumann deleted the gmx_run_unit branch

September 23, 2024 08:54

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