diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
index f3ae58e..4548c9b 100644
--- a/.github/workflows/gh-pages.yml
+++ b/.github/workflows/gh-pages.yml
@@ -38,6 +38,8 @@ jobs:
run: src/python/build_site.py
- name: Create overview
run: bmp-create-overview --html-file=_site/index.html
+ - name: Create reports
+ run: python3 vis/generate_petab_reports.py --output-dir=_site/reports
- name: Setup Pages
uses: actions/configure-pages@v5
- name: Upload artifact
diff --git a/src/python/pyproject.toml b/src/python/pyproject.toml
index 7629cf2..d0959cc 100644
--- a/src/python/pyproject.toml
+++ b/src/python/pyproject.toml
@@ -28,7 +28,7 @@ dependencies = [
[project.optional-dependencies]
dev = ["pre-commit", "pytest", "ruff"]
-site = ["bokeh>=3.7.3"]
+site = ["bokeh>=3.7.3", "petab[vis]", "Jinja2>=3.0.3"]
[project.scripts]
bmp-petablint = "benchmark_models_petab.check_petablint:main"
diff --git a/vis/generate_petab_reports.py b/vis/generate_petab_reports.py
new file mode 100755
index 0000000..8c2d417
--- /dev/null
+++ b/vis/generate_petab_reports.py
@@ -0,0 +1,97 @@
+import argparse
+import base64
+import io
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import pandas as pd
+import petab.v1
+import petab.v1.visualize.plotter
+from jinja2 import Environment, FileSystemLoader
+from petab.visualize import plot_problem
+
+import benchmark_models_petab as bmp
+
+# plot simulation line without markers
+petab.v1.visualize.plotter.simulation_line_kwargs["marker"] = ""
+# plot measurements with markers only
+petab.v1.visualize.plotter.measurement_line_kwargs["linestyle"] = "None"
+
+
+def _plot_problem(problem: petab.v1.Problem, sim_df: pd.DataFrame) -> str:
+ """Plot measurement points and simulation line for one observable and return base64 png."""
+ plot_problem(problem, simulations_df=sim_df)
+ fig = plt.gcf()
+
+ buf = io.BytesIO()
+ fig.savefig(buf, format="png", dpi=150)
+ plt.close(fig)
+ buf.seek(0)
+ img_b64 = base64.b64encode(buf.read()).decode("ascii")
+ return img_b64
+
+
+def generate_report_for_model(problem_id: str, template_env: Environment, out_dir: Path):
+ problem = bmp.get_problem(problem_id)
+ if problem is None:
+ return
+
+ sim_df = bmp.get_simulation_df(problem_id)
+
+ images: list[dict[str, str]] = []
+ img = _plot_problem(problem, sim_df)
+ images.append({"id": problem_id, "img": img})
+
+ template = template_env.get_template("problem_report.html.jinja")
+ rendered = template.render(model_name=problem_id, images=images)
+
+ out_dir.mkdir(parents=True, exist_ok=True)
+ out_path = out_dir / f"{problem_id}.html"
+ with open(out_path, "w", encoding="utf-8") as fh:
+ fh.write(rendered)
+ print(f"Wrote {out_path}")
+
+
+def generate_index(problem_id_list: list[str], template_env: Environment, out_dir: Path):
+ """Render an index page with links to per-problem reports."""
+ template = template_env.get_template("index.html.jinja")
+ rendered = template.render(models=problem_id_list, count=len(problem_id_list))
+
+ out_dir.mkdir(parents=True, exist_ok=True)
+ out_path = out_dir / "index.html"
+ with open(out_path, "w", encoding="utf-8") as fh:
+ fh.write(rendered)
+ print(f"Wrote {out_path}")
+
+
+def main(output_dir: Path = None):
+ if output_dir is None:
+ output_dir = Path(__file__).parent / "reports"
+ templates_dir = Path(__file__).parent / "templates"
+
+ env = Environment(loader=FileSystemLoader(templates_dir), autoescape=True)
+ problem_id_list = list(bmp.MODELS)
+
+ for problem_id in problem_id_list:
+ try:
+ generate_report_for_model(problem_id, env, output_dir)
+ except Exception as e:
+ print(f"Skipping {problem_id} due to error: {e}")
+
+ try:
+ generate_index(problem_id_list, env, output_dir)
+ except Exception as e:
+ print(f"Failed to write index: {e}")
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(description="Generate PETab problem reports")
+ parser.add_argument(
+ "--output-dir",
+ "-o",
+ type=Path,
+ default=None,
+ help="Directory to write reports to (default: vis/reports)",
+ )
+ args = parser.parse_args()
+
+ main(args.output_dir)
diff --git a/vis/templates/index.html.jinja b/vis/templates/index.html.jinja
new file mode 100644
index 0000000..910bd5d
--- /dev/null
+++ b/vis/templates/index.html.jinja
@@ -0,0 +1,26 @@
+
+
+
+
+ PEtab problems overview
+
+
+
+ PEtab problems ({{ count }})
+ {% if models %}
+
+ {% for m in models %}
+ - {{ m }}
+ {% endfor %}
+
+ {% else %}
+ No problems found.
+ {% endif %}
+
+
diff --git a/vis/templates/problem_report.html.jinja b/vis/templates/problem_report.html.jinja
new file mode 100644
index 0000000..932fb02
--- /dev/null
+++ b/vis/templates/problem_report.html.jinja
@@ -0,0 +1,38 @@
+
+
+
+
+
+ {{ model_name }} - PEtab report
+
+
+
+
+
+ {{ model_name }}
+ {% if images %}
+ {% for img in images %}
+
+ {% endfor %}
+ {% else %}
+ No observables or data available for this problem.
+ {% endif %}
+
+
+