Commit Graph

2917 Commits

Author SHA1 Message Date
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
Alyssa Travitz
8cc3c4f291 cli gather should allow lists of filepaths (#1212)
* allowing multiple paths

* first pass at allowing filepaths and wildcards

* updating docstring

* adding missing /

* add tests and sorting

* add news

* updating docstring

* updating docs

* fixing whitespace diff

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
2025-04-07 07:13:08 -07:00
Alyssa Travitz
be13099aee fix formatting 2025-04-04 16:27:24 -07:00
Alyssa Travitz
d7f89cd6e2 making it look better in sphinx 2025-04-04 10:41:09 -07:00
Alyssa Travitz
f58e5372ec fix cli list formatting 2025-04-04 10:22:50 -07:00
Alyssa Travitz
939a7bdd29 moving under the hood to the user guide (#1221)
* moving under the hood to the user guide

* adding pip to docs env dependencies
2025-04-03 12:19:12 -07:00
Alyssa Travitz
e46ff925a3 fix docker build workflow (#1220)
* fixing singularity help and version calls

* bump build-push-action to v6

* bump docker-cron build-push-action to v6
2025-03-31 14:15:01 -07:00
Alyssa Travitz
fde3b1697f add PR 1210 to changelog (#1218) v1.3.1 2025-03-27 15:46:16 -07:00
Alyssa Travitz
e0885fdcac Updated CHANGELOG for 1.3.1 (#1216)
* Updated CHANGELOG for 1.3.1

* Update docs/CHANGELOG.rst

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* Apply suggestions from code review

edits from mikemhenry

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* formatting

* adding PR #

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
2025-03-27 15:30:49 -07:00
Alyssa Travitz
cd219bc002 only show --allow-partial suggestion if user hasn't used it (#1208)
* only show --allow-partial suggestion if user hasn't used it

* adding a test
2025-03-27 13:31:16 -07:00
Mike Henry
35aa3aab52 bump disk space for gpu runner (#1209)
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
2025-03-27 08:13:37 -07:00
Alyssa Travitz
01c3b5601e 1002: improve missing data error handling (#1199)
* add check for missing protocol result data

* renaming vars for  clarity

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
2025-03-27 07:18:30 -07:00
Alyssa Travitz
e044ec4a61 pooch - add triplicate retries (#1213)
* add triplicate retries

* use openfe cache

* add internet check to openfe

* isort as a treat

* whitespace :(

* remove unused pytest.mark.download
2025-03-26 14:54:27 -07:00
Alyssa Travitz
66ac2bdc64 migrate json loading to new gufe syntax (#1177)
* updates to cli from_json

* replacing dump instances with to_json

* Remove unnecessary imports of JSON_HANDLER

* addressing review

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: David L. Dotson <dotsdl@gmail.com>
2025-03-25 23:32:26 +00:00
Alyssa Travitz
37448403e3 switch kcal/mol to kilocalorie_per_mole for roundtrip consistency (#1210)
* switch kcal/mol to kilocalorie_per_mole

* add test
2025-03-25 12:46:03 -07:00
Alyssa Travitz
1213d06704 adding changlog entry for 1112 (#1207) 2025-03-25 07:04:42 -07:00
Ethan Holz
429138a318 ci: update to the new start and stop actions (#1201)
* ci: add support for new start/stop runners for GPU runner job

This commit utilizes the new OMSF start/stop gha-runner action for the
gpu_runner workflow.

* ci: add support for new start/stop runners for CPU runner job

This commit utilizes the new OMSF start/stop gha-runner action for the
cpu_runner workflow.
2025-03-24 12:51:58 -07:00
Alyssa Travitz
b798454425 1104 gather check json files (#1112)
* adding output for failed edges

* adding print statements, tests don't pass yet because of extra output

* remove straggler

* Update openfecli/commands/gather.py

Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>

* comment out exception check temporarily

* adding exception check back (test data was wrong)

* adding tests in progress

* trying different mocking

* adding unit tests

* cleaning up

* updating zenodo doi to use correct parallel rbfe dataset

---------

Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk>
2025-03-19 17:53:00 +00:00
Alyssa Travitz
a823546bab fix rbfe parallel results dataset (#1196)
* placeholder

* move to new zenodo community
2025-03-18 13:54:15 -07:00
Mike Henry
651a574386 remove deps in pyproject.toml (#1191) 2025-03-14 14:42:42 -07:00
Alyssa Travitz
31bb2a777d make gufe lowercase in docs (#1190)
* make gufe lowercase in docs

* Update docs/reference/index.rst

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* Update docs/reference/api/index.rst

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
2025-03-14 09:55:24 -07:00
Mike Henry
c5d0e58e58 Make get gpu info more robust (#1186)
* Handel case where nvidia-smi returns "no gpus found"

* blacl

* handle more error codes, and then add a wild card match

* blacked

* make sure we return {} if we hit an error

* added tests for system probe

* black

* added news entry
2025-03-12 11:15:22 -07:00
Irfan Alibay
384d9ccb4b Merge pull request #1174 from OpenFreeEnergy/chunk_limit
Temporary solution for #1173
2025-03-10 13:39:02 +00:00
IAlibay
61afac5933 Merge branch 'chunk_limit' of github.com:OpenFreeEnergy/openfe into chunk_limit 2025-03-10 10:46:33 +00:00
IAlibay
9546bdbd07 Add some docs 2025-03-10 10:46:24 +00:00
Irfan Alibay
ac69e730d0 Merge branch 'main' into chunk_limit 2025-03-10 10:24:17 +00:00
Irfan Alibay
97329605cf Merge pull request #1183 from OpenFreeEnergy/relax-interchange-pin
Unpin interchange since we have a new openmmff release
2025-03-07 23:12:07 +00:00
Irfan Alibay
fc33b0b2da Merge branch 'main' into relax-interchange-pin 2025-03-07 17:01:32 +00:00
Irfan Alibay
51da376768 Remove handle_trajectories (#1182)
* Remove handle_trajectories

* Add news item
2025-03-07 09:50:25 -07:00
Mike Henry
60f708bbd8 Unpin interchange since we have a new openmmff release 2025-03-07 09:08:45 -07:00