* Update docstrings, run in CI
* Do not necessarily assume ff14SB port is installed
* Remove some references to `simtk`
$ grep -r simtk . | wc -l
0
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>
When copying the gaff dat file to the temporary directory to avoid
spaces in the path, also use a fixed file name, 'gaff.dat', in case of
spaces in the file name too.
Change out of temporary directory before raising an exception that
causes the directory to be deleted as the context manager exits. If not
done, a PermissionError is raised repeatedly on Windows and the
message from the original exception is very difficult to read. This
behaviour was observed for the parmchk2 command, but the fix has also
been applied to the antechamber command.
Unnecessary % sign in the parmchk2 command string sometimes gets filled
with junk characters on Windows and stops the command from running
successfully. This behaviour only occurs on some Windows systems and
does not occur on Linux or Mac.
