finish substrate rename fix

Check that the pkpd flag was supplied before renaming the substrate.

Full Changelog: studio-pkpd-v1.0.7...studio-pkpd-v1.0.8

Fix bug in substrate rename

Check that the pkpd flag was supplied before renaming the substrate.

Full Changelog: studio-pkpd-v1.0.6...studio-pkpd-v1.0.7

Fix bug in pk csv element tag names

Full Changelog: studio-pkpd-v1.0.5...studio-pkpd-v1.0.6

Fix rules change on rename; track upstream

Track recent updates in upstream.

Fix bug (I made it) in updating rules on renaming cells or substrates.

Full Changelog: studio-pkpd-v1.0.4...studio-pkpd-v1.0.5

studio-pkpd-v1.0.4

Make PK tab prettier (at least not a complete mess). CSV path support. SBML folder support.

Full Changelog: studio-pkpd-v1.0.3...studio-pkpd-v1.0.4

Constant PKs

Now can set constant PKs. Using a CSV file as before for 1C and 2C models, specify the times at which the circulation concentration changes, i.e. the times at which the Dirichlet conditions change. The first column of the csv is the times the concentration changes. The second column is the value it changes to. The concentration will stay fixed at that value until the next time it is set.

Also includes changes to upstream studio between January 2024 and May 2024, including the BIWT.

Full Changelog: studio-pkpd-v1.0.2...studio-pkpd-v1.0.3

Incorporate base studio vis_tab update

Include a minor update from PhysiCell-Studio upstream branch tweaking the vis_tab.

Full Changelog: https://github.com/drbergman/PhysiCell-Studio/commits/studio-pkpd-v1.0.2

Robustness against alternate XML formats

Puts the same check in pkpd_populate_tree_cell_defs as in populate_tree_cell_defs for making sure subelements of cell_definitions are cell_definition's.

Full Changelog: studio-pkpd-v1.0.0...studio-pkpd-v1.0.1

Studio with PhysiPKPD

A version of PhysiCell-Studio that can also configure PK and PD models for use with PhysiPKPD. Run studio with the --pkpd flag.

To get started with your own project do the following:

• Download the attached python script
• Rename to get_physipkpd.py
• Run with python get_physipkpd.py (will set up a folder called PhysiPKPD_Project that is ready to use with PhysiPKPD from its development-rules-integration-studio-version branch that integrates with this release)
• Run make pkpd-template to load up the template project
• Run python [path-to-this-studio] -c ./config/pkpd_model.xml -e pkpd_model --pkpd

get_physipkpd.txt