GitHub / openforcefield/openff-toolkit / commits
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
| SHA | Message | Author | Date | Stats |
|---|---|---|---|---|
| ec093f91 | Mambaforge -> Miniforge (#2253) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
7 days ago | |
| 948844b8 | Minor grammar fixes in in AI policy (#2252) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
8 days ago | |
| 3760dbe9 | Use `python-constraint2` (#2251) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
10 days ago | |
| 1ebb0748 |
Document OFFXML string sources for ForceField (#2250)
Co-authored-by: Jeff Wagner <j****l@g****m> Signed-off-by: Atharva Tilewale <1****e@u****m>, Atharva Tilewale <1****e@u****m>, Atharva Tilewale <1****e@u****m> |
Atharva Tilewale <1****e@u****m>
Committed by: GitHub <n****y@g****m> |
10 days ago | |
| ef074d58 |
Add AI policy, update PR template (#2248)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
21 days ago | |
| 2aba3042 |
Stop OpenEyeToolkitWrapper from erroring on planar trivalent nitrogens if the...
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
21 days ago | |
| b3ad73d5 |
Fix CI (#2249)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
21 days ago | |
| 278cc811 |
[pre-commit.ci] pre-commit autoupdate (#2245)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
pre-commit-ci[bot] <6****]@u****m>
Committed by: GitHub <n****y@g****m> |
about 1 month ago | |
| cccef076 |
Add support for QCSchema v2 and test on Python 3.14 (#2238)
Co-authored-by: Jeff Wagner <j****l@g****m> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
about 1 month ago | |
| f4566b86 |
Use file name comparisons when finding force fields to load (#2236)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
about 2 months ago | |
| a1e74cb7 | Fix some Pydantic V2 deprecations in tests (#2234) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
about 2 months ago | |
| e2d05cc7 | More gently fail if AmberTools provenance fails (#2230) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
about 2 months ago | |
| a9355325 | add pytest-timeout to conda/deployment test envs (#2229) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| d97dd2ec | 0.19.0 postrelease |
Jeff Wagner <j****l@g****m>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 3673715c |
Add AshGC to `Molecule.assign_partial_charges` docstring (#2185)
Co-authored-by: Jeffrey Wagner <j****l@g****m> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 01308a54 |
Bump richardsimko/update-tag from 2 to 3 (#2228)
Co-authored-by: dependabot[bot] <4****]@u****m> Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 88301b1a |
Stringify `None` in `ParameterType.to_dict` (fix issue #2150) (#2225)
Co-authored-by: Ashley Mitchell <y****i@g****m>, Ashley Mitchell <y****i@g****m> |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 83787a9a | disable beta/rc ci (#2227) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 4fa2f7c0 | Require RDKit in CI (#2215) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| f1f99ab7 | Add reruns to notebooks in CI (#2226) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
3 months ago | |
| 2bfd5eed | Update deployment testing envs (#2219) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
4 months ago | |
| 7911500e | Update examples to use Sage 2.3.0, so make rdkit+nagl required and drop OE ex... |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
4 months ago | |
| f98d20a1 |
[pre-commit.ci] pre-commit autoupdate (#2212)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
pre-commit-ci[bot] <6****]@u****m>
Committed by: GitHub <n****y@g****m> |
4 months ago | |
| 3f48c8f0 | Test without `typing_extensions` explicitly declared (#2211) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
4 months ago | |
| f2317d1c |
Add code of conduct (#2210)
Co-authored-by: jaclark5 <j****k@o****g>, Jeff Wagner <j****l@g****m> |
Jennifer A Clark <j****k@o****o>
Committed by: GitHub <n****y@g****m> |
4 months ago | |
| 120f7147 |
Bump actions/checkout from 6 to 7 (#2206)
Co-authored-by: dependabot[bot] <4****]@u****m> Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 805861b8 | Switch to `setuptools-scm` (#2201) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 2167db44 | un-down-pin numpy in testing envs (#2199) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| ec7cf885 | Fix `ForceField.label_molecules` docstring (#2156) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| b397de35 |
Fix pytest config, warnings (#2170)
Co-authored-by: Copilot <1****t@u****m>, Copilot <1****t@u****m> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 3f9a673e | 0.18.1 post release |
Jeff Wagner <j****l@g****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 29732ccc | 0.18.1 release prep |
Jeff Wagner <j****l@g****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| d0f206a6 |
Bump codecov/codecov-action from 6 to 7 (#2196)
Co-authored-by: dependabot[bot] <4****]@u****m> Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 0c16be07 |
Add support for N-terminal, protonated, disulfide-bonded cysteine (#2194) (#2...
Co-authored-by: Joe Laforet Jr. <7****t@u****m> |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 8e39c98f |
Fix #2182 (CI failing) (#2187)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 8fa2c79b |
Bump richardsimko/update-tag from 1 to 2 (#2188)
Co-authored-by: dependabot[bot] <4****]@u****m> Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
5 months ago | |
| 6e2fc352 |
Drop support for Python 3.11 (#2174)
Co-authored-by: mattwthompson <7****n@u****m>, Matt Thompson <m****n@o****g>, copilot-swe-agent[bot] <1****t@u****m>, mattwthompson <7****n@u****m>, Jeff Wagner <j****b@o****g> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
6 months ago | |
| b56ac244 |
[pre-commit.ci] pre-commit autoupdate (#2169)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
pre-commit-ci[bot] <6****]@u****m>
Committed by: GitHub <n****y@g****m> |
7 months ago | |
| 1f972262 |
Bump mamba-org/setup-micromamba from 2 to 3 (#2167)
Co-authored-by: dependabot[bot] <4****]@u****m> Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
7 months ago | |
| 59c8d9b3 |
Bump codecov/codecov-action from 5 to 6 (#2166)
Co-authored-by: dependabot[bot] <4****]@u****m> Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
7 months ago | |
| 9b6189d1 |
Remove most stability/suitability/experimental warnings (#2120)
Co-authored-by: Jeff Wagner <j****b@o****g>, Jeffrey Wagner <j****l@g****m> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
8 months ago | |
| 5b91bcdf |
Bump Interchange to 0.5 in tests and examples (#2163)
Co-authored-by: Jeff Wagner <j****b@o****g>, Jeff Wagner <j****b@o****g>, Jeff Wagner <j****l@g****m> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
8 months ago | |
| c70bda93 | Fix README link checks (#2165) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
8 months ago | |
| 329a5c8b | Improve `Molecule.remap` docstring (#2160) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
8 months ago | |
| 7c738b26 |
update citation instructions in readme (#2158)
Co-authored-by: Jeff Wagner <j****b@o****g>, Matt Thompson <m****n@p****m>, Jeff Wagner <j****b@o****g> |
James R. Baggs Eastwood <j****d@g****m>
Committed by: GitHub <n****y@g****m> |
8 months ago | |
| 1828a877 | pin xmltodict <=1.0.2 in CI (#2151) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
9 months ago | |
| 1017880c | Treat ParmEd as optional dependency in tests (#2145) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
10 months ago | |
| 436b7f1a | Update README and disable Zenodo link checks in CI (#2147) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
10 months ago | |
| 4dd0dcd8 |
[pre-commit.ci] pre-commit autoupdate (#2140)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
pre-commit-ci[bot] <6****]@u****m>
Committed by: GitHub <n****y@g****m> |
10 months ago | |
| 311608b1 | Fix conda CI (#2139) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
10 months ago | |
| 8f25ca2f | Fix examples CI (#2137) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
11 months ago | |
| 73d62fec | Remove installer action (#2135) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
11 months ago | |
| c109ae3f | Fix package data (#2127) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
11 months ago | |
| 7351b5ed |
Bump actions/upload-artifact from 5 to 6 (#2133)
Co-authored-by: dependabot[bot] <4****]@u****m> Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
11 months ago | |
| 10c2d5a3 | add workflow dispatch triggers to latest and examples CI |
Jeff Wagner <j****l@g****m>
Committed by: GitHub <n****y@g****m> |
11 months ago | |
| e92ed596 | Add back "True-True" CI (#2123) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
12 months ago | |
| 97ba5699 | Treat NAGL as an optional dependency (#2121) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
12 months ago | |
| d7b6ed80 | Update mixture simulation example (#2125) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
12 months ago | |
| 6d455a5c |
Bump actions/checkout from 5 to 6 (#2126)
Co-authored-by: dependabot[bot] <4****]@u****m> Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
12 months ago | |
| 95a463fc | 0.18.0 post release |
Jeff Wagner <j****l@g****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| f63576a2 |
Speedup for molecule isomorphism checking (#2114)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 7febf6d5 |
Bump actions/upload-artifact from 4 to 5 (#2116)
Co-authored-by: dependabot[bot] <4****]@u****m> Signed-off-by: dependabot[bot] <s****t@g****m> |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 832755ae | Avoid poor scaling of OEChem coordinate lookup (#2115) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 69fe926a |
[pre-commit.ci] pre-commit autoupdate (#2112)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m>, Matthew W. Thompson <m****n@p****m> |
pre-commit-ci[bot] <6****]@u****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| eea73dca | 0.17.1 postrelease |
Jeff Wagner <j****l@g****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 8e616636 |
Format `pyproject.toml` (#2111)
Co-authored-by: Jeff Wagner <j****l@g****m> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 2a66046e | Change tests that expect smirnoff99Frosst ffs to not expect them (#2109) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 76ffd161 | Raise an error when loading a PDB file would lead to mangled atom order (#2107) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 5b4941c7 | Declare minimum Python version (#2097) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| e3912617 | Update conformer energies example (#2101) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 3ded9791 | 0.17.0 post release |
Jeff Wagner <j****l@g****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 9f29507a |
Actually format with `ruff` (#2085)
Co-authored-by: Jeffrey Wagner <j****l@g****m>, pre-commit-ci[bot] <6****]@u****m> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| d70974de |
Implement NAGLChargesHandler (#2048)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 143a70fe | Bump actions/checkout from 4 to 5 (#2094) |
dependabot[bot] <4****]@u****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| 8d4c8f25 |
Improve some typing (#2000)
Co-authored-by: Matthew W. Thompson <m****n@p****m> |
Josh A. Mitchell <y****i@g****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 25570d0f | update for 0.16.10 |
Jeff Wagner <j****l@g****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 893f3b63 | prepare releasehistory for 0.16.10 release (#2091) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 2bf586e0 | Improve speed of quantity stringification (#2090) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 158117d5 |
[pre-commit.ci] pre-commit autoupdate (#2080)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m>, Jeff Wagner <j****l@g****m> |
pre-commit-ci[bot] <6****]@u****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| d5d4cf8e |
Issue molecule notebook (#2078)
Co-authored-by: jaclark5 <j****k@o****g> |
Jennifer A Clark <j****k@o****o>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 54f74020 | fix 2075 (#2076) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 838e2f52 | Update Python versions badge (#2074) |
Irfan Alibay <I****y@u****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| cbd1d43c | Drop `cached-property` (#2067) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 55f2413a |
Drop use of `importlib_metadata` (#2054)
Co-authored-by: Jeff Wagner <j****l@g****m> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 5502b4eb |
Lazy evaluation of the amber toolkit version (#2066)
Co-authored-by: Jeff Wagner <j****l@g****m> |
Vladimir Mironov <v****v@u****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 71588978 | Constrain NumPy < 2.3 in tests (#2070) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 713cfa90 | Fix 2051 (#2052) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| fc6402fb | 0.16.9 post release |
Jeff Wagner <j****l@g****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| d4e8cef9 | releasenotes cleanup (#2049) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| e735c2b2 |
Speed up identical molecule detection (#2025)
Co-authored-by: Josh A. Mitchell <y****i@g****m>, Josh A. Mitchell <y****i@g****m> |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| f4fff548 | Add CODEOWNERS file (#2046) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 834c9fea | Test examples on 3.11 and 3.12 (#2043) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| a9faad77 | Drop testing on Python 3.10 (#2041) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| cd2198dc |
[pre-commit.ci] pre-commit autoupdate (#2042)
Co-authored-by: pre-commit-ci[bot] <6****]@u****m> |
pre-commit-ci[bot] <6****]@u****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| ca7231bc | Support large molecule InChi with RDKit (#2040) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| ef71eda9 | Catch MissingOptionalDependencyError when nglview is not installed (#2039) |
Evan Pretti <p****i@s****u>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 4cc57064 | re-ignore external examples in conda tests (#2038) |
Jeff Wagner <j****b@o****g>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 7d753eba | Test on Python 3.13 (#2029) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 5ee02399 |
Drop Parmed-requiring examples (#2032)
Co-authored-by: Jeff Wagner <j****b@o****g>, Jeff Wagner <j****b@o****g> |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 467b8f2a | Do not use development-facing `openff-units` (#2030) |
Matt Thompson <m****n@p****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago |