Automate creation of PBPK model reports

[Yuri05]

Create GH-Action for creation of evaluation reports and projects

• Create it in a separate branch (e.g. CreateReports)
• The action should be triggered either on demand or after pushing into the CreateReports branch

Inputs:

1. Table (e.g. CSV file) with repository names and model versions to be used

Execute	Repository name	Released version	Snapshot name (default: same as repository name)	Workflow name (default: Evaluation/workflow.R)	Additional projects
X	7E3-Model	1.0	7E3
X	BAY794620-Model	1.0	BAY794620
X	CDA1-Model	1.0	CDA1
X	dAb2-Model	1.0	dAb2
X	Digoxin-Model	2.0
X	Inulin-Model	1.0	Inulin
X	MEDI524-Model	1.0	MEDI524
X	MEDI524YTE-Model	1.0	MEDI524YTE
X	Propofol-Model	1.0	Propofol	evaluation/Workflow.R
X	Tefibazumab-Model	1.0	Tefibazumab

2. Table (e.g. CSV file) with the release versions of the software

Tool	Version
OSP Suite	12.0_beta1
Qualification Runner	11.1
Reporting Engine	2.2.367
Qualification Framework	3.2

Workflow

1. Install the tools (OSP Suite / Quali Runner / RE ) from the releases provided above

2. For each model provided in the table: I. Download the released model version with the release number provided above

   • Either from the tag of the release (e.g. 7E3-Model | 1.0 ▶️ https://github.com/Open-Systems-Pharmacology/7E3-Model/releases/tag/v1.0)
   • Or from the release archive (e.g. 7E3-Model | 1.0 ▶️ https://github.com/Open-Systems-Pharmacology/7E3-Model/archive/refs/tags/v1.0.zip)

   II. Switch to the model workflow folder and execute workflow.R passing the versions of the OSP Suite, Quali Framework and Model release which are used

   III. If the report created is not called <model_name>_evaluation_report.md - rename it (e.g. compare https://github.com/Open-Systems-Pharmacology/OSP-PBPK-Model-Library/tree/master/Alfentanil)

   IV. Create the pdf version of the report <model_name>_evaluation_report.pdf

   • Use the OSP pdf CSS

   V. Create the PK-Sim project .pksim5

   • Ideally, the qualification runner should get an option to create a PK-Sim project. Until it's not possible: PK-Sim CLI can be used for that

   VI. (Optionally): Create additional PK-Sim projects (e.g. like Alfentanil-Pediatrics.pksim5 here

3. Get the develop branch of the repository

4. For each model with successfully created evaluation report: replace the content of the <model-name> subfolder with the newly created reports and projects.

5. Create a pull-request into the develop branch

6. If some of the reports failed: the status of the GH-Action should be failed and the list of the failed projects should be shown in the annotations

[Yuri05]

Some additional thoughts/ideas:

• Instead of using a released version of a model, we could allow also using the current development version (e.g. by using the dev keyword in the model table info.

Execute	Repository name	Released version	Snapshot name (default: same as repository name)	Workflow name (default: Evaluation/workflow.R)	Additional projects
X	7E3-Model	dev	7E3

or branch (main, master, whatsoever)