Alyssa Travitz
2ecb01dd2d
CLI interface IS redundant
2024-11-12 11:10:21 -08:00
Alyssa Travitz
69f2d0b25b
capitalize YAML
2024-10-18 11:24:17 -07:00
Alyssa Travitz
bbc535f14d
moving Kartograf link)
2024-10-16 08:43:35 -07:00
Alyssa Travitz
24ef319523
clarity edits to cli_yaml docs
2024-10-16 08:23:09 -07:00
Alyssa Travitz
15394414e2
formatting fixes to cli_basics
2024-10-16 07:44:19 -07:00
Irfan Alibay
83028b132f
Merge pull request #955 from OpenFreeEnergy/fix_slow_cli_call
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move slow import inside function call
2024-10-12 20:42:06 +01:00
Alyssa Travitz
0186b3ce92
move slow import inside function call
2024-10-11 16:16:48 -07:00
pre-commit-ci[bot]
29d8cd9ba0
[pre-commit.ci] pre-commit autoupdate ( #950 )
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updates:
- [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0 )
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2024-10-07 15:51:43 -07:00
Mike Henry
35b5f12d2e
bump apptainer version ( #949 )
2024-10-04 08:43:48 -07:00
Irfan Alibay
521c7d87ef
Merge pull request #945 from OpenFreeEnergy/fix-tmp-files-tests
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Fix errand files being created during tests
2024-09-30 08:32:42 +01:00
IAlibay
6b917204f7
Add tmpdir call to test
2024-09-29 22:33:28 +01:00
Irfan Alibay
015f34e113
Merge pull request #940 from OpenFreeEnergy/update-zenodo
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Update CITATION.cff
2024-09-25 23:57:58 +01:00
IAlibay
1672985f75
All the pins
2024-09-25 23:31:51 +01:00
Mike Henry
1aaa37f325
pin micromamba version
2024-09-25 15:10:59 -07:00
IAlibay
7db0c4147f
Updated CHANGELOG for 1.1.0
2024-09-25 22:53:08 +01:00
Irfan Alibay
c66a969a67
Update CITATION.cff
2024-09-25 22:49:06 +01:00
Irfan Alibay
f4475bfe47
Merge pull request #937 from OpenFreeEnergy/hotfix-struct-analysis
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Hotfix: structural analysis
2024-09-18 03:33:05 +01:00
IAlibay
f4a79308ac
Add test for the error return
2024-09-18 03:05:43 +01:00
IAlibay
5bc9f964ac
Add some comments
2024-09-17 18:26:08 +01:00
IAlibay
6022f4ec62
Add news entry
2024-09-17 02:12:58 +01:00
IAlibay
8c5cfe5909
improve test a little bit even if it's wrong
2024-09-17 02:00:58 +01:00
IAlibay
e16f21fb01
add a few basic checks on the npz contents
2024-09-17 01:57:37 +01:00
IAlibay
39cd94672d
Fix path parsing
2024-09-17 00:41:20 +01:00
IAlibay
efd7c23419
Fix spurious file writing in tests
2024-09-17 00:30:12 +01:00
IAlibay
d9cba9a0de
Add some fixes
2024-09-17 00:13:40 +01:00
IAlibay
731463ff2b
where -> shared change
2024-09-16 23:04:45 +01:00
IAlibay
10b019cc4e
rename a few things
2024-09-16 22:59:17 +01:00
IAlibay
651247b9e4
move things to npz
2024-09-16 22:55:25 +01:00
IAlibay
2531b9aaf0
It's going to be a long night
2024-09-16 22:35:32 +01:00
Irfan Alibay
117ce98369
Merge pull request #930 from OpenFreeEnergy/perses_mapper
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Perses mapper
2024-09-16 19:11:43 +01:00
Josh Horton
78d67c94b9
Merge remote-tracking branch 'origin/perses_mapper' into perses_mapper
2024-09-16 16:36:00 +01:00
Josh Horton
cd90bdca60
add news
2024-09-16 16:35:48 +01:00
Irfan Alibay
66d878f3b1
Update test_perses_atommapper.py
2024-09-16 08:31:12 +01:00
Josh Horton
79de2e8454
update perses atom mapper to use openff units
2024-09-10 14:59:51 +01:00
Josh Horton
3fe9d43bfb
update doc string
2024-09-05 12:30:44 +01:00
Josh Horton
eba4f71c6c
update unit type hints, add dict round trip test
2024-09-05 11:17:36 +01:00
Josh Horton
075e07e65c
lint
2024-09-04 11:52:27 +01:00
Josh Horton
b2cdc30159
add abstract methods for PersesAtomMApper, activate tests
2024-09-03 16:26:57 +01:00
Irfan Alibay
733908d245
Merge pull request #928 from OpenFreeEnergy/removing_empty_file
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removing empty file, the content was moved to gufe.
2024-09-03 08:26:52 +01:00
riesben
0394417bc6
removing empty file, the content was moved to gufe.
2024-09-03 09:03:34 +02:00
Irfan Alibay
c4951c0e54
Some AWS CI updates ( #910 )
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* Update gpu-runner.yaml
* test on a g4dn.xlarge @ 53 cents an hour
* testing on a p2.xlarge @ 90 cents an hour
* Update gpu-runner.yaml
* Update gpu-runner.yaml
* update AMI to correct region (still the 'Deep Learning Base OSS Nvidia Driver GPU AMI' AMI)
* fix default shell, yolo that there is no syntax issues
* use the _REAL_ correct default shell
* Add a timeout of 12 hrs instead of the default 6
* Added oe toolkit + espaloma_charge to GPU env for testing
* fix channel name
* got a download error on the cudatoolkit shim which we don't want anyway
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
2024-08-27 14:40:24 +00:00
Irfan Alibay
5745e5eaa5
Merge pull request #673 from OpenFreeEnergy/noncubic-solvent
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OpenMMSolvation: Support for non-cubic boxes and defined box properties
2024-08-27 15:00:05 +01:00
Mike Henry
a9d8fb5816
Merge branch 'main' into noncubic-solvent
2024-08-27 06:21:44 -07:00
Irfan Alibay
24248e5c0b
Merge pull request #923 from OpenFreeEnergy/fix/doi-lookup-fail
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Rerun test if we get a DOI lookup error
2024-08-27 12:41:27 +01:00
Irfan Alibay
80d2a7438c
Merge branch 'main' into noncubic-solvent
2024-08-27 12:35:06 +01:00
Mike Henry
271dcda18a
Rerun test if we get a DOI lookup error
2024-08-23 17:59:53 -07:00
Irfan Alibay
2712c70485
Merge pull request #922 from mattwthompson/patch-1
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Bump minimum Python version to 3.10
2024-08-22 20:54:14 +01:00
Matt Thompson
9eb036d2ea
Bump minimum Python version to 3.10
2024-08-22 14:33:24 -05:00
IAlibay
a90bd695a6
Add news entry
2024-08-21 14:48:37 +01:00
Irfan Alibay
7a9d6f98c0
Merge branch 'main' into noncubic-solvent
2024-08-13 20:53:56 +01:00
