* test if CI is green
* github has removed macos-12 runners
* something is weird with the ambertools build on macos-13
* test new ambertools 23 build
* try older build
* test new ambertools build
* bump ci
* update the openmm versions we test
* don't test on intel macs
* re-enable gaff
* run espaloma and gaff tests
* gaff has two fs michael
* Use 8.1.2rc1
* Update linters
* Remove Espaloma tests
* Apply suggestions from code review
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
* working on parmchk output
* fix pytest warnings
* Migrate from pkg_resources to importlib_resources
* Remove shipping gaff/ffxml and read everything from parmchk2
* make sure we use older openmm version for testing
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* test on ci now
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* decided to keep shipping the xmls
* cleaned things up, gave a better name to the set we track gaff atom types
* Update openmmforcefields/generators/template_generators.py
* updated change log
* Added note about how we might remove openmmforcefields/ffxml/amber/gaff/ffxml in a future release
---------
Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* re-enable gaff
* run espaloma and gaff tests
* gaff has two fs michael
* Use 8.1.2rc1
* Update linters
* Remove Espaloma tests
* Apply suggestions from code review
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
* Use Intel macOS runners
* check if older macos works
* test all the macos versions
* see if rdkit is the issue
* Drop macOS 13
* Typo/fix
* Update dependencies
---------
Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
* Temporarily remove GAFF because of parmchk2 issues
* Drop OpenEye from tests
* Drop automerge action
* Update Python and AmberTools versions, run tests in parallel
* Remove Espaloma from test environment
* Remove Espaloma CI
* Refactor some tests to enable skipping GAFF
* Skip SPC/E test when iterating over small molecule force fields
* Update default force field in `SystemGenerator`
* Streamline testing
* Update testing setup
* Mask CodeCov upload failures
* Add release notes
* Scattered fixes
* Pin AmberTools
* Skip non-small molecule force fields at test time
* Always run tests, even if OpenEye is not licensed
* OPC
* Update Python versions
* Trim more force fields at test time
* Parametrize tests
* Revert "Parametrize tests"
This reverts commit 5b37af526f.
* Debug, comments
* Run all tests
* Testing espaloma in different workflow
* pinning dgl version
* Change name of workflow
* Testing espaloma only with latest openff toolkit
* using pytest and fixtures
* Marking espaloma tests and parametrizing
* Running espaloma tests in workflow
* Fixing call in test
* Cache test should be inside context manager
* Remove support for older openff toolkit (<0.11)
* Specifying root path for tests
* testing without the /
* fixing CI yamls
* Mark espaloma tests
* need argument for tests
* remove trailing newline
---------
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* conversion script from openmm #3773
* add converted ions from ambertools-22.0-py38h6177452_1
* OPC and OPC3 water (without ions) from openmm #3654
* move opc waters
* fix typo
* make opc and opc3 standard files by combining water and ions
* Fix paths
* Fiddle with paths again
* Bring in openff-amber-ff-ports by default
* Move `opc.xml` and `opc3.xml`
Co-authored-by: Alex Izvorski <aizvorski@gmail.com>
* make sure we don't install the newest toolkit by mistake
* make sure we don't pull in a really old version of the toolkit
* forgot to add a verb there
* Start to make internals compatible with both unit packages
* Try different logic
* Improve logic in test
* Fix some tests
* Fix
* Fix
* Better units logic in tests
* Remove temporary code
* That's too semantic a variable name
Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>
* 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>
* 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
* Drop 3.7, add 3.10
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* Update ci.yaml
* kill CI when another job is triggered on the same PR and don't upload codecov on scheduled runs
* use cuda shim
* update torch
* update *py*torch
