15 Commits

Author SHA1 Message Date
Matt Thompson
54e6e4099e Add uniform, automated linting (#319)
* Add uniform, automated linting

* Remove code paths that use old OpenFF Toolkit API

* Re-lint

* Switch to ruff

* Fix

* Fix bad merge

* Another lint
2024-05-03 10:48:05 -07:00
Mike Henry
35496e5095 Fix toolkit tests (#227)
* Ensure 0.11.0 RC version of toolkit is installed

* Possible fix to finish #191

* Try to ensure bash args thing is passed through

* Naive unit refactor

* Work through tests

* Update CI matrix

* Use mamba for development

* Debug, add boilerplate .gitignore

* Fix syntax

* make sure the package didn't get installed before we install it

* Do not install Espaloma

* Fix some unit registries in tests

* install espaloma, but remove openmmforcefields

* add back in espaloma

* switch to micromamba

* Explicitly move ffxml sources into entry point

* Remove symlinking

* Add boilerplate `.gitignore`

* Update package installation in CI

* Fix finding Amber files in test

* Soft import whatever units module is used by the toolkit

* Switch to micromamba for setting up conda environment

Add boilerplate `.gitignore` file

Do not pull from non-standard labels

Install instead of update

Try to figure out why if: {{ false }} still triggers

Syntax?

Tinker

Bring in (full) mamba

Bash thing everywhere

Bring down old toolkit

Do not present un-loadable ff14SB port as available

More pins

* Fix YAML syntax

* Use pip

* More fixes

* No particles
* Fix unit serialization
* Fix Atom.element calls

* Update some tests

* Clean up un-used imports

* Fix more tests

* Fix more tests

* Exclude Python 3.10 on macOS

* Skip ff14SB being treated as a small molecule

* Fix test

* Track duration of longest 20 tests

* Update action versions

* Try to fix exclusions in CI matrix

* Fix pathing in Amber conversion

* Run `pyupgrade --py38-plus`

* Try directly uploading coverage report

* Fix syntax

* Add back some tests

* Debug

* Drop `pytest-xdist` arg

* Fiddle with path

* Just try to get stuff passing

* Try uploading again

* Switch back to codecov

* Simply coverage reporting

* Allow 0 coverage

* Simplify coverage arguments

* Add `__init__.py` in `/tests/` submodule

https://stackoverflow.com/a/60579142

* Add `__init__.py` in `/tests/` submodule

https://stackoverflow.com/a/60579142

* Simplify coverage arguments

* Add back durations argument

* Apply suggestions from code review

* only upload report if it is not scheduled

Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>
2022-09-15 20:59:04 +00:00
John Chodera
2ab75f849e Migrate GAFF to amber/gaff/{ffxml,dat} 2019-11-29 18:02:43 -05:00
John Chodera
c85f458105 Update AMBER force fields with AmberTools 19.9 2019-11-29 16:32:10 -05:00
John Chodera
89b1328b5a Update generators and setup.py 2019-11-29 11:58:40 -05:00
John Chodera
862a3dcf10 Update test environment. 2019-10-29 22:11:21 -07:00
John Chodera
cb3efa0b9f Upadate paths 2019-10-26 20:21:50 -07:00
John Chodera
be575a6250 Fix issues with tests 2019-10-26 19:43:47 -07:00
John Chodera
8d5bdee59d Update to MolSSI cookiecutter 2019-10-26 18:55:15 -07:00
jchodera
059ab28cdf Add ambertools dependency; remove build-time dependencies 2017-09-29 17:26:10 -04:00
John Chodera
db415b6768 Try to get tests to run on travis 2017-06-23 23:17:36 -04:00
John Chodera
a50fba557f Update setup to install tests subpackage 2017-06-23 22:48:34 -04:00
John Chodera
eb66ee4dcb AMBER installation works; added tests 2017-06-23 22:27:50 -04:00
John Chodera
f4e0a908d1 Fix typo 2017-06-23 15:03:52 -04:00
John Chodera
2ee2b22ed6 Initial draft of setup.py and autodiscovery 2017-06-23 14:57:03 -04:00