Add gather support for parallel dir structure #1044

atravitz · 2024-12-09T20:25:07Z

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This reverts commit 6ae5d1d.

…er_support_parallel_dir_structure

github-actions · 2024-12-09T20:25:22Z

🚨 API breaking changes detected! 🚨

github-actions · 2024-12-09T20:28:02Z

🚨 API breaking changes detected! 🚨

github-actions · 2024-12-12T00:21:08Z

🚨 API breaking changes detected! 🚨

github-actions · 2024-12-12T00:41:14Z

🚨 API breaking changes detected! 🚨

IAlibay

Couple comments on the protocol side of things, not read the rest yet.

openfe/protocols/openmm_rfe/equil_rfe_methods.py

codecov · 2024-12-12T00:48:21Z

Codecov Report

Attention: Patch coverage is 90.00000% with 5 lines in your changes missing coverage. Please review.

Project coverage is 92.73%. Comparing base (76127a1) to head (f4e753a).
Report is 136 commits behind head on main.

Files with missing lines	Patch %	Lines
openfecli/commands/gather.py	77.27%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1044      +/-   ##
==========================================
- Coverage   94.57%   92.73%   -1.84%     
==========================================
  Files         135      135              
  Lines       10061    10077      +16     
==========================================
- Hits         9515     9345     -170     
- Misses        546      732     +186

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github-actions · 2024-12-12T15:31:21Z

🚨 API breaking changes detected! 🚨

github-actions · 2024-12-12T15:38:38Z

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github-actions · 2024-12-13T17:03:46Z

🚨 API breaking changes detected! 🚨

github-actions · 2024-12-13T18:43:40Z

🚨 API breaking changes detected! 🚨

github-actions · 2024-12-13T19:23:09Z

🚨 API breaking changes detected! 🚨

news/support_gather_parallel.rst

hannahbaumann

Thanks @atravitz , this looks great. Only thing I'm not so sure about yet is the input file path for gather.
I wanted to test this on one of my old result files, however they were in a structure such as this:
all_results with following subfolders:
results_0, results_1, results_2, results_other_setting_0, results_other_setting_1, results_other_setting_2.
If I only want to analyze the results from the first three folders, I'd have to move the other folders in a different directory.
This could be fine, but alternatively, gather could also take a list of Paths. I'm not sure yet what is better, but just wanted to raise this use case.

openfe/protocols/openmm_rfe/equil_rfe_methods.py

IAlibay · 2024-12-17T13:52:46Z

gather could also take a list of Paths.

Just wanted to chime in here that having gather take in a list of results JSON and/or directories would be great (the former more than the latter)! That being said I do think this is maybe something to be dealt with elsewhere.

Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>

atravitz · 2024-12-18T23:36:32Z

I agree with both of you @IAlibay @hannahbaumann - how do you feel about me addressing this in a follow-up PR?

hannahbaumann

Thanks @atravitz , lgtm!

github-actions · 2024-12-20T16:38:34Z

No API break detected ✅

atravitz and others added 7 commits December 9, 2024 08:52

add docstrings

a1a5c4b

Revert "add docstrings"

735a474

This reverts commit 6ae5d1d.

adding fixture

192a5d4

whitespace fixes

637c576

added (failing) test for parallel results data

270b5b5

add back all report types into testing

6bf8a0d

Merge branch 'main' of github.com:OpenFreeEnergy/openfe into add_gath…

a9d50d3

…er_support_parallel_dir_structure

include serial and paralell in paramterize

09e4232

atravitz linked an issue Dec 9, 2024 that may be closed by this pull request

gather should support simulation repeats submitted in parallel #987

Closed

atravitz added 2 commits December 11, 2024 12:29

adding support for raw output type

636d010

expose uncertainty and estimate functions to gather

709e517

pass dGs through - works but isn't pretty

a6103df

IAlibay reviewed Dec 12, 2024

View reviewed changes

remove todo

030e85c

Merge branch 'main' into add_gather_support_parallel_dir_structure

9071208

atravitz requested review from mikemhenry and removed request for mikemhenry December 12, 2024 16:16

atravitz changed the title ~~[WIP] Add gather support for parallel dir structure~~ Add gather support for parallel dir structure Dec 12, 2024

atravitz marked this pull request as ready for review December 12, 2024 16:46

atravitz requested a review from mikemhenry December 12, 2024 16:46

Merge branch 'main' into add_gather_support_parallel_dir_structure

f9a34d5

updating changelog

38d2f2c

updating changelog

8d966d4

atravitz mentioned this pull request Dec 13, 2024

refactor the CLI #1056

Open

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atravitz commented Dec 13, 2024

View reviewed changes

news/support_gather_parallel.rst Show resolved Hide resolved

atravitz requested review from hannahbaumann and jthorton and removed request for mikemhenry December 13, 2024 23:38

hannahbaumann reviewed Dec 17, 2024

View reviewed changes

openfe/protocols/openmm_rfe/equil_rfe_methods.py Outdated Show resolved Hide resolved

hannahbaumann self-assigned this Dec 17, 2024

Update openfe/protocols/openmm_rfe/equil_rfe_methods.py

47a9b8c

Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>

atravitz and others added 2 commits December 18, 2024 15:36

Merge branch 'main' into add_gather_support_parallel_dir_structure

a0bebb8

fix type hint

6ec1dcb

atravitz mentioned this pull request Dec 18, 2024

gather should support a list of paths #1064

Closed

hannahbaumann approved these changes Dec 19, 2024

View reviewed changes

Merge branch 'main' into add_gather_support_parallel_dir_structure

f4e753a

atravitz merged commit 66476fd into main Dec 20, 2024
11 checks passed

atravitz deleted the add_gather_support_parallel_dir_structure branch December 20, 2024 17:05

Add gather support for parallel dir structure #1044

Add gather support for parallel dir structure #1044

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