Christopher Woods

Fn http api reveals values of "fn config app" variables to anyone, which may reveal secrets

4

I've been building an Fn application with functions that have to hold authentication info to connect to a central object store. I passed the login secrets to the Fn functions...

Feature web (a.k.a. BioSimSpace 2023.0.0)

16

This is the update of BioSimSpace that is compatible with Sire 2023.0.0. The changes are minimal, i.e. updating to using the new (PEP8) module names of sire (but not the...

Add support for CMAP terms and chamber files

2

Issue for myself to remind me that we need to add support for CMAP terms and chamber files (and the CHARMM forcefield generally) to the AmberPrm parser. This will be...

A suggestion prompted by a reviewer - add a function that sorts loaded trajectory frames in different ways, e.g. could sort based on the timestamp of the trajectory files, the...

Add support for reading Gromacs FEP topology files

2

While we can write Gromacs FEP topology files for merged molecules, we cannot read back those files. We should add support for reading Gromacs topology files that contain merged molecules.

[BUG] Update cmake version as upcoming deprecation

2

We currently set `cmake_minimum_required` to `3.3.0`. CMake support for

Adding updateSomeParametersInContext to optimise parameter updates

1

This PR adds in `updateSomeParametersInContext` to complement the existing `updateParametersInContext` functions of the Force classes (with a corresponding `copySomeParametersToContext` added to the force kernels, complementing `copyParametersToContext`). The use case for...