Known issues and to-dos

[bbye98]

General

• Figure out how to upload MDCraft to the conda-forge channel.
• Prepare manuscript for the Journal of Open Source Software (JOSS).
• Update documentation ("Welcome" page, "Getting started" guide, etc.) and add examples.
• Add contributor guidelines.
• Write more unit tests to bring code coverage up to 80%.

Analysis submodule

• Add time blocking (n_blocks argument) support, when appropriate, for analysis modules that support outputting results as a functions of time.
• Verify that unwrapping is necessary and/or implemented correctly in the analysis.electrostatics, analysis.polymer, and analysis.transport modules.
• Allow dimension-specific (axes argument) dipole moment calculations in analysis.electrostatics.DipoleMoment.
• Check validity of unwrapping/wrapping in the analysis.profile module.
• Only store, use, and evaluate dimensions specified in axes in analysis.profile.DensityProfile for faster performance.
• Allow non-cubic/triclinic box dimensions in analysis classes, when appropriate.
• Investigate massive drop-off in performance in analysis.structure.IntermediateScatteringFunction.

OpenMM submodule

• Check whether the FENE bond potential in openmm.bond.fene is working correctly.