openff-evaluator

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Being able to monitor the Dask dashboard remotely is a useful feature. I can do this currently with: ``` function dashboard { address=$1 port=$2 dest=${3:-hpc3} ssh -N -f -L 127.0.0.1:${port}:${address}:${port}...

lilyminium

**Daemon workers and dask config** I tried to set up a DaskSLURMBackend and received this error: ``` distributed.worker - WARNING - Compute Failed Function: _wrapped_function args: (, 'evaluator_working-data/SimulationLayer/f4683d534fda4bd6bb6d8722fafff554/456cf9ec8e1649c1a15d61042b188733_build_solvated_coordinates', '{"id": "456cf9ec8e1649c1a15d61042b188733|build_solvated_coordinates",...

lilyminium

`from_pandas` and `from_json` methods of `PhysicalPropertyDataSet` object return different objects

2

The `from_pandas` method of the `openff.evaluator.datasets.PhysicalPropertyDataSet` object returns an instance of the `PhysicalPropertyDataSet` object, but the `from_json` method returns a dictionary. These methods should both return the same object to...

ocmadin

[PAPRIKA] Host-Guest Free Energy Gradients

5

## Description This PR adds support for calculating the free energy gradients for host-guest systems with the `paprika` protocol. ## Status - [ ] Ready to go

jeff231li

Calculate density expectation as M/<V> instead of M<1/V>

1

I'd argue that M/\ instead of M is a better quantity to be calculating. Volume is the more fundamental thermodynamic quantity (dG/dP = V), and the numerical behavior is better...

mrshirts

Replace the internal AttributeXXX classes with attrs

1

From @SimonBoothroyd: The current `AttributeClass` and `Attribute` classes were mainly created to be flexible representations of data classes to be used when speccing out the new class designs as part...

dotsdl

updates: - [github.com/psf/black: 24.4.2 → 24.8.0](https://github.com/psf/black/compare/24.4.2...24.8.0) - [github.com/PyCQA/flake8: 7.1.0 → 7.1.1](https://github.com/PyCQA/flake8/compare/7.1.0...7.1.1) - [github.com/nbQA-dev/nbQA: 1.8.5 → 1.8.7](https://github.com/nbQA-dev/nbQA/compare/1.8.5...1.8.7)

pre-commit-ci[bot]

Specified skip_on_failure=True

5

To make paprika_testing work with pydantic version 2.xx, the `root_validator` decorator needs to specify skip_on_failure=True. ## Todos Notable points that this PR has either accomplished or will accomplish. - [X]...

jaketanderson

Weighting in excess properties done by ThermoML mole fractions rather than simulation mole fractions

8

**Describe the bug** What we seem to be observing is that when you compute an excess property, and you do the calculation (for enthalpy for example), then with $H_{mixing} =...

mrshirts

## Description https://docs.pydantic.dev/latest/changelog/#v11018-2024-08-22 ## Todos Notable points that this PR has either accomplished or will accomplish. - [ ] Use v1-compatible `from pydantic.v1` import ## Status - [ ] Ready...

mattwthompson