PhysiCell

PhysiCell copied to clipboard

responsive to #355 previously used the cell type ID (an integer) to fill in the __. Want to use the name of the cel type though.

drbergman

Standardize how all files are copied to output. This serves several purposes: - ensures that the config file is copied - previously handled in user-defined `main.cpp` - now done in...

drbergman

We had only looked for the Linux/MacOS pathsep (`'/'`) to identify the basename for the file being copied to the output folder. If a user set this with a Windows...

drbergman

simplified dc functions

1

The current API for the Dirichlet nodes is inconsistent and confusing (See #214). To simplify the API for users, I have created two functions that handle all the DC logic...

drbergman

@heberlr first identified this behavior and a discussion led to opening #347. While better handling of thrown exceptions would be an improvement, for now have this error behave like all...

drbergman

Low priority PR that fixes bug causing intracellular updates to skip the first diffusion time step at t=0. I don't believe that PhysiBoSS or PhysiCelldFBA require this step to be...

drbergman

In models with both `pre_update_intracellular` and `post_update_intracellular` functions, it is currently possible for some cells to complete their post-update before other cells begin their pre-update. If the post-update modifies values...

drbergman

Improve librr api

2

The key improvement here is the **automated** linking of PhysiCell values and SBML values through the config file (NO CUSTOM CODING REQUIRED!!). It does introduce a breaking change in that...

drbergman

provide a CSV file with similar structure to the substrate ICs csv header row: x,y,z,,,... where the list of substrates need not be all the substrates, only those with DCs...

drbergman

Pull Request: Adds functionality to stop and restart a simulation without losing information, even when using the Physiboss add-on The main changes include: - I/O streaming operator added in the...

Danariki99