pub_soft/openfe
3
0
Fork 0
mirror of https://github.com/OpenFreeEnergy/openfe.git synced 2026-06-08 08:54:25 +08:00
Code Issues Packages Projects Releases Wiki Activity
3,366 Commits 151 Branches 46 Tags
cli/refactor_quickrun_result
Commit Graph

10 Commits

Author SHA1 Message Date
Alyssa Travitz
b693d37c8a ruff: address pycodestyle changes (#1668) 
* apply E741: ambiguous variable name check

* apply E713: 'not in' fixes

* address E721 with isintance() checks

* fix bare excepts

* precommit
 2025-11-11 11:34:29 -07:00
Alyssa Travitz
588f552ca9 add ruff isort linting rule (#1665) 
* isort for docs and utils

* isort for top-level openfe, analysis, setup

* isort setup/

* isort storage/

* isort protocols

* isort openn_afe

* isort openmm_rfe

* isort all protocols

* apply isort to openfe/tests

* apply isort to openfecli

* apply isort to devtools/

* add TODO for setup init
 2025-11-10 21:58:30 +00:00
Alyssa Travitz
2311a2f2d9 ruff formatting part 2 - everything but the tests (#1610) 
* add more checks

* make precommit manual

* apply formatting to pyproject.toml

* add TODO

* remove unneeded, add a few more

* add ruff, but turn everything off

* add openfe known first party

* format highest-level files

* first half of openfe protocols

* second half of openfe protocols

* openfe protocols formatting, with alyssa's fmt skips

* add ruff formatter to precommit

* fmt: off all vendored _rfe_utils code

* addressing review comments

* format openfe/utils

* format openfe/setup

* first batch of cli formatting

* second batch of cli formatting

* formatting the rest of openfecli commands

* format openfecli/parameters

* format openfe/storage

* run precommit

* Update openfecli/commands/gather.py

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

* update example notebooks branch for v1.7.0 docs changes (#1615)

* bump example notebooks branch

* add ipykernel to env

* roll back to fixing septop branch

* i dont think we want ipykernel

* bump to tmp_fix_docs branch

* point to branch revert-237-v1.7_cookbooks

* point to latest example notebooks release

* remove colab button, point to updated example notebooks, reorg landing page (#1618)

* remove colab button from example notebooks in docs

* point to example notebooks 2025.10.2

* replace 'try' with CLI

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
 2025-10-24 14:09:45 -07:00
David W.H. Swenson
4e0a50b86b Update logging; final tests 2023-07-31 16:35:24 -05:00
David W.H. Swenson
65bc171411 testing things involving root logger is hard 2023-07-31 14:45:09 -05:00
David W.H. Swenson
ce02a988d5 use stdout for our INFO loggers 2023-07-27 12:07:34 -05:00
David W.H. Swenson
93b002d2a6 updates to logging (esp around quickrun) 2023-07-27 11:43:56 -05:00
riesben
a3a3ea2ac4 mutated to func decorator 2023-04-10 10:51:36 +01:00
David W.H. Swenson
6447b917b9 Update based on review comments 
Still need to add tests for this. Also, it looks like DummyProtocol
isn't doing any file output here ... need to figure out why
 2022-10-24 10:27:49 -05:00
David W.H. Swenson
41068e0185 CLI for AtomMapping (#57) 
* Initial skeleton for the CLI

Currently requires the OPS CLI to be installed as well; next steps:

1. Add parameter core classes to infrastructure
2. Fully separate infrastructure into its own package

* switch to using plugcli

* tests for CLI

* helps if you add the tests...

* pep8 and deps cleanup

* add test_plugins

* Start of CLI atommapping report

* Add tests for parameters

* Almost-working atommapping command

* add hack to work-around lomap issue

* fix test

* pep8; docstrings; add header comments

* Add tests for commands/atommapping

* docstrings

* add init to command to stop circular import error

* remove init and it still works?

Co-authored-by: richard <richard@nextmovesoftware.com>
 2022-02-23 16:43:01 +00:00