David L. Dotson
David L. Dotson
## Description Addresses #591 Pydantic models support direct JSON serialization; we take advantage of this here to support use of e.g. sets in a model. The `to_json` and `from_json` methods...
**Is your feature request related to a problem? Please describe.** It is often the case that the initial `maxiter` setting for geometry optimization datasets is set too low on submission,...
**Describe the bug** The indices used for datasets submitted to QCArchive are forced to lowercase, and this can cause problems for e.g. SMARTS used as the indices, in which two...
**Is your feature request related to a problem? Please describe.** There are cases in which e.g. `Molecule`s have been submitted previously, but now we want them to have additional metadata...
**Describe what you are trying to achieve** The `"OpenFF Fragmenter Validation 1.0"` `TorsionDriveDataset` has several `"INCOMPLETE"` `OptimizationRecords`. We believe these to be broken in some way, though it is not...
**Describe the bug** Installing `qcfractal` sets testing options `--runslow` and `--runexamples` for pytest globally (within the conda env). This can cause hard-to-diagnose problems for testing of other packages, in particular...
When attempting to install `openmm` via `conda` with: ``` conda create -n openmm -c conda-forge "python=3.10.*" openmm ``` This yields on Arch Linux 64-bit: ``` Collecting package metadata (current_repodata.json): done...
## Description A nonequilibrium cycling protocol supporting execution with OpenMM, using the protocol structure defined in [`gufe`](https://github.com/OpenFreeEnergy/gufe). ## Motivation and context This is one of the first protocols to be...
This PR addresses #80. We have added an `alchemlyb.preprocessing.bootstrapping` submodule. The functions exposed by this module should work on both `dHdl` and `u_nk` standard forms, with a similar usage feel...
Consistent with how we instruct users in [our docs](https://alchemlyb.readthedocs.io/en/latest/estimators.html), we should [avoid using `iloc`](https://github.com/alchemistry/alchemlyb/pull/201#issuecomment-1170613385) and instead use `.loc` in our tests to specify which states to get free energy differences...