Fix OpenMM unit utils API regression #445
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mattwthompson
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May 13, 2022
Updates for units and element refactors Empty commit to trigger CI Fix typo More updates for elemennt & unit updates Update test environment Debug curl failure Fix atom filtering Update atom indexing Remove meaningless assignment Revert checkmol debugging Lint Update test env Fixes for new virtual site behavior Possible fixes for Yank layer Fix labelling molecules with virtual sites Fix OpenMM unit utils API regression (#445) Update release notes for 0.3.11 Black conf.py Move to openff theme Add dependencies to rtd environment Modernise RTD config Update documentation build instructions Fix docs env path Small fixes and typos Add openff-units to RTD environment
mattwthompson
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Jul 19, 2022
* Refactor to use draft of toolkit v0.11.0 * Updates for units and element refactors * Empty commit to trigger CI * Fix typo * More updates for elemennt & unit updates * Update test environment * Debug curl failure * Fix atom filtering * Update atom indexing * Remove meaningless assignment * Revert checkmol debugging * Lint * Update test env * Fixes for new virtual site behavior * Possible fixes for Yank layer * Run CI on v0-3-x branch * Run `pre-commit autoupdate` * Update unit formatting in test, pin Pint >=0.19 * Fixed typo of "Aromatic" (#432) * Replace Behaviour with Behavior (#409) * /behaviour/behavior/ * don't subclass * Lint Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com> * Refactor out the use of cmiles Fix syntax * # This is a combination of 15 commits. # This is the 1st commit message: Refactor to use draft of toolkit v0.11.0 # This is the commit message #2: Updates for units and element refactors # This is the commit message #3: Empty commit to trigger CI # This is the commit message #4: Fix typo # This is the commit message #5: More updates for elemennt & unit updates # This is the commit message #6: Update test environment # This is the commit message #7: Debug curl failure # This is the commit message #8: Fix atom filtering # This is the commit message #9: Update atom indexing # This is the commit message #10: Remove meaningless assignment # This is the commit message #11: Revert checkmol debugging # This is the commit message #12: Lint # This is the commit message #13: Update test env # This is the commit message #14: Fixes for new virtual site behavior # This is the commit message #15: Possible fixes for Yank layer * Refactor to use draft of toolkit v0.11.0 Updates for units and element refactors Empty commit to trigger CI Fix typo More updates for elemennt & unit updates Update test environment Debug curl failure Fix atom filtering Update atom indexing Remove meaningless assignment Revert checkmol debugging Lint Update test env Fixes for new virtual site behavior Possible fixes for Yank layer Fix labelling molecules with virtual sites Fix OpenMM unit utils API regression (#445) Update release notes for 0.3.11 Black conf.py Move to openff theme Add dependencies to rtd environment Modernise RTD config Update documentation build instructions Fix docs env path Small fixes and typos Add openff-units to RTD environment * Remove support for `simtk` namespace * Fixes * Pin to newer Pint * Test against toolkit PR #1276 * Simplify CI until passing * Fix OpenMM positions tests * Fix another OpenMM positions test * Cherry-pick #448 * Remove lint workflow, replaced by `pre-commit` * Fix CI workflow * Update toolkit branch * Fix writing OpenMM quantities to Yank files * Fiddle with molecule labeling * Add "How to cite" section" * Update environments with RC packages * Fix environments * Typo * Toggle stereochemistry filter * Fix * Update docs env * Fix * Fix nested access to parameter types * Do not assume vdW parameters accessible in library charge subset * Turn off stereochemistry check when loading SMILES to Component https://github.com/openforcefield/cmiles/blob/83d2463d61c7d6837d83086c2fd91fae59feb2ae/cmiles/utils.py#L74-L79 * Update tests for fixed stereochemistry filtering * Draft release notes for 0.4.0 * Revert another stereochemistry test * Update test workflow * Try relaxing Python pin in docs build * Always use RDKit for molecule -> SMILES * Force PDB writer to use RDKitToolkitWrapper Co-authored-by: Jake Anderson <jta002@ucsd.edu> Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com> Co-authored-by: Author: Xia, Yu <xiayu.x@bytedance.com>
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Description
This PR fixes the API regression caused by removing the
openmm_quantity_to_pintandpint_quantity_to_openmmAPI points thatforcebalancerequires.Status