Commit Graph

2946 Commits

Author SHA1 Message Date
Mike Henry
fc822c859d Merge branch 'main' into qa-script 2025-05-27 13:53:39 -07:00
Alyssa Travitz
8ade13d9fe cleaning up and formatting network planning tests (#1304)
* cleaning up and formatting network planning tests

* updating fixture scopes

* removing fixture scope

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
2025-05-27 13:20:23 -07:00
Alyssa Travitz
098c0a8a84 updating syntax for click 8.2 (#1276) 2025-05-27 18:35:44 +00:00
Mike Henry
67e33fa448 fix syntax with conda-lock (#1292)
* fix syntax with conda-lock

* don't run these while we are testing since it just eats up runners

* not sure how I messed up that command

* undo ci skip

* skip running other CI

* test lf env

* fix prefix location

* fix syntax with conda-lock

* don't clone the repo to get the latest tag

* fix yaml syntax

* forgot to include id

* test on osx as well

* osx /home -> /Users

* cleanup language

* update name

* propagate name change
2025-05-27 11:14:07 -07:00
Mike Henry
d2e84eef9e Exit with return value from pytest.main (#1297)
* exit with the return value of pytest.main when running openfe test

* always restore env
2025-05-27 08:27:04 -07:00
Irfan Alibay
9626bbf4c5 Merge pull request #1289 from OpenFreeEnergy/afe_base_update
Small FF assignment refactor of the AFE base unit class
2025-05-23 15:34:06 +01:00
Mike Henry
14d56333d9 Merge branch 'main' into afe_base_update 2025-05-23 07:17:04 -07:00
Mike Henry
592845c582 Feat/add lock file (#1290)
* way better way to do this

* get the names right

* fix syntax with action

* fix syntax with action
2025-05-23 06:39:05 -07:00
IAlibay
23218d5f16 Small FF assignment refactor of the AFE base unit class 2025-05-23 11:25:22 +01:00
Irfan Alibay
9af2e4b585 Merge pull request #1286 from OpenFreeEnergy/news_1275
News for AFE box fix
2025-05-22 18:20:18 +01:00
IAlibay
6e40f0f32c News for AFE box fix 2025-05-22 13:42:21 +01:00
Irfan Alibay
5b1d3de8a8 Merge pull request #1275 from OpenFreeEnergy/afe-box-fix
Add box vector fix to AFE base
2025-05-22 12:11:31 +01:00
Irfan Alibay
9cbf7aad05 Merge branch 'main' into afe-box-fix 2025-05-22 10:54:32 +01:00
Mike Henry
d3e60487aa now we handle systems where there is a charge change 2025-05-21 12:01:44 -07:00
Alyssa Travitz
0bd14c7b79 add retries for flaky notebooks (#1278) 2025-05-21 17:11:16 +00:00
Curtis Colwell
5c44c39d5d Remove duplicate line in environment.yml (#1280) 2025-05-21 16:52:18 +00:00
Alyssa Travitz
e4cced26c3 updating nb name (#1281) 2025-05-21 09:28:10 -07:00
Mike Henry
251ba90d7e first pass on a QA script 2025-05-21 08:07:15 -07:00
Alyssa Travitz
395ed35837 update notebook names (#1279) 2025-05-20 13:04:46 -07:00
Irfan Alibay
907cdfd477 Merge branch 'main' into afe-box-fix 2025-05-16 17:50:53 +01:00
Irfan Alibay
7f44e5f581 Add Alyssa to citations file. (#1274)
* Add Alyssa to citations file.

* Update CITATION.cff
2025-05-16 09:02:29 -07:00
IAlibay
251a7cf222 fix things 2025-05-15 20:01:36 -04:00
IAlibay
a2a663ca5b add fix 2025-05-15 18:59:23 -04:00
Mike Henry
d21f7360e1 Pin click to <8.2.0 until we fix tests (#1271) 2025-05-12 12:56:26 -07:00
Alyssa Travitz
8fe616d421 move openmm test data from figshare to zenodo (#1270) 2025-05-09 09:45:08 -07:00
Alyssa Travitz
148af2694c Update cli docs (#1264) 2025-04-30 13:46:11 -07:00
Alyssa Travitz
2d2fef2a07 Fix docs version (#1262)
* only use major and minor version in docs

* add issue number in comment

* updating version parsing
2025-04-29 11:03:32 -07:00
Irfan Alibay
10536f846b Merge pull request #1256 from OpenFreeEnergy/add_rich_dep
adding rich as a dependency
2025-04-28 10:32:49 +01:00
Alyssa Travitz
3f7c9df23a adding rich as a dependency 2025-04-25 09:09:00 -07:00
Alyssa Travitz
9296aa7fb0 Release prep 1.4.0 (#1253)
* Updated CHANGELOG for 1.4.0

* changing a word

* fixing formatting

* adding links (thanks mike)

* adding links

* adding description

* updating changelog
v1.4.0
2025-04-25 07:02:27 -07:00
Alyssa Travitz
b6c7f19c81 immediate print planning cli output (#1254)
* immediate print planning cli output

* adding news item
2025-04-24 14:35:03 -07:00
Alyssa Travitz
3dc10653d1 require -o option for CLI charge generation (#1255)
* require -o option for charge generator

* adding a test for missing -o
2025-04-24 14:08:12 -07:00
Alyssa Travitz
e42432d5b0 pretty print tables with rich (#1246)
* add pandas construction

* removing csv writer

* replicating original behavior

* add rich table

* split into function

* make names clearer

* adding adjustments from rebase

* put it in a box

* adding tsv flag

* update tests to use tsv flag

* add smoke test for pretty print

* adding file creation test

* adding news item

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
2025-04-24 10:02:26 -07:00
Irfan Alibay
6b3f501fa2 Merge pull request #1250 from OpenFreeEnergy/docs/sphinx_theme_v02
pin to ofe-sphinx-theme v0.2.0
2025-04-24 15:13:07 +01:00
Irfan Alibay
630034aa28 Merge branch 'main' into docs/sphinx_theme_v02 2025-04-24 07:39:05 +01:00
Alyssa Travitz
36f5fb8387 pin to ofe-sphinx-theme v0.2.0 2025-04-23 19:56:57 -07:00
Alyssa Travitz
d43d8c1324 making a news entry more clear (#1249)
* making news entry more clear

* fix code chars
2025-04-23 19:45:27 -07:00
Alyssa Travitz
0e21b35b00 Clean up tutorial index (#1233)
* switch to concise bulleted list for clarity

* updating description
2025-04-23 15:52:46 -07:00
Alyssa Travitz
98f6a98e8f add news entry for 1245 (#1248) 2025-04-23 15:38:56 -07:00
Alyssa Travitz
aedc719aa5 Single repeat error handling (#1243)
* fail on first leg with too few repeats

* pass through all failed edges

* adding news entry

* improve error message

* fix test
2025-04-23 17:58:21 +00:00
Alyssa Travitz
38f0c6a3ef print message to stderr when no valid results files are found (#1245)
* print message to stderr when no valid results files are found

* fix check

* move check into main function to keep single responsibility

* fix cmet test bug

* adding test
2025-04-23 17:33:52 +00:00
Alyssa Travitz
1bbe2d9299 use pandas (#1244)
* add pandas construction

* replicate current behavior, but with pandas

* removing csv writer

* fixing type check

* replicating original behavior
2025-04-23 09:23:06 -07:00
Alyssa Travitz
d811614e8c fixing test's allow partial test (#1247) 2025-04-23 07:44:10 -07:00
Alyssa Travitz
e640424817 Pass through failed simulations to output (#1227)
* reorg for clarity

* moving try/except into function for clarity

* reorg data parsing for clarity

* remove unused function

* add try/except to pass through info about failed edges

* updating tests for new expected failed simulation checking behavior

* pass through for raw and ddg

* pass through failures for dgs

* remove unused import

* adding a missing check

* docstrings

* cleaning up logic

* cleaning up logic

* docstrings and formatting

* fixing conditionals bug

* more docstrings

* make 'name' a tuple for consistency

* make functions private

* updating output statement for clarity (hopefully)

* remove unused dg raw expected output

* adding comment description

* updating tests

* cleaning up test to not use tmp dir

* only use non-None legs for deciding whether to do rbfe/rhfe

* fix typo

* pass empty list instead of None through to ddg

* add cmet data

* add assert success tests - still need output validation

* light reordering for clarity

* adding pytest regressions

* don't include stderr in file regression

* making output more legible

* switch from runtime error to exit(1)

* add missing complex legs test

* adding regressoin tsvs  to manifest

* reordering functions for clarity

* updating tests

* adding test for disconnected network

* updating warning message, not throwing error for now

* updating tests for missing runs

* add disconnected network check

* switch from NaN to Error

* removing unused regression files

* fixing typo

* adding test coverage

* fix typo

* adding news entry
2025-04-22 07:24:31 -07:00
Curtis Colwell
767ac6ea18 Alphabetize environment.yaml (#1235)
* Alphabetize environment.yaml

Have been having some dependency issues. Noticed numpy in there twice.

* Complete alphabetization

---------

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
2025-04-18 08:09:57 -07:00
Mike Henry
c2fbaeee6e Switch to setuptools_scm (#1237) 2025-04-17 11:06:09 -07:00
Irfan Alibay
28ab53a452 Merge pull request #1225 from OpenFreeEnergy/fix/charge_molecules_cli_formatting
fix cli settings help message formatting
2025-04-16 14:26:30 +01:00
Irfan Alibay
534ba1fe19 Merge branch 'main' into fix/charge_molecules_cli_formatting 2025-04-16 14:09:37 +01:00
Alyssa Travitz
5808444fa5 pin numpy to <2.0 (#1230) 2025-04-14 12:04:41 -07:00
Alyssa Travitz
0dfa9a2e50 Merge branch 'main' into fix/charge_molecules_cli_formatting 2025-04-07 07:14:02 -07:00