Commit Graph

9 Commits

Author SHA1 Message Date
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
Alyssa Travitz
9f386ab933 Update CLI help messages (#1265)
* updating misc help messages

* add view ligand network help message and docstirng

* minor language changes

* whitespace :(

* fixing whitespace
2025-06-05 13:12:02 -07:00
David W.H. Swenson
eb8d08a199 Reorganize CLI command section grouping 2023-05-10 11:56:32 -04:00
David W.H. Swenson
7ecb920103 Add --log parameter
A lot of this was taken from the OpenPathSampling CLI.

See openpathsampling/openpathsampling-cli#15
2022-12-06 14:53:46 +00:00
David W.H. Swenson
333628efff Expose loaders in CLI (#200) 2022-10-27 15:56:33 -05:00
Mike Henry
a0cefa42fc don't need to import openfe anymore now 2022-03-04 13:44:23 -07:00
Mike Henry
fdc895f310 use versioneer for the version number 2022-03-04 11:08:25 -07:00
David W.H. Swenson
a6c973fcdc Add --version to CLI (#75) 2022-03-03 11:01:55 +00:00
David W.H. Swenson
ea64274813 CLI Skeleton (#49)
* 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
2022-02-16 11:46:15 +00:00