Skip to content

Add PEtab SciML example notebook #3208

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
BSnelling merged 5 commits into from
Jul 15, 2026
Merged

Add PEtab SciML example notebook #3208

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
eba5f44
add petab sciml notebook
BSnelling Jul 10, 2026
f08f0ee
clear output from sciml notebook
BSnelling Jul 15, 2026
efb044d
add petab sciml dep
BSnelling Jul 15, 2026
734c792
with torch as well
BSnelling Jul 15, 2026
feb4740
use cdn for file fetch
BSnelling Jul 15, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 5 additions & 0 deletions .github/workflows/test_python_cplusplus.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -239,6 +239,11 @@ jobs:
- name: Install python package
run: scripts/installAmiciSource.sh

- name: Install torch (for PEtab-SciML notebook)
run: |
source ./venv/bin/activate \
&& python -m pip install "petab_sciml[torch] @ git+https://github.com/petab-dev/petab_sciml.git@main"
Comment thread
dweindl marked this conversation as resolved.

- name: example notebooks
run: scripts/runNotebook.sh doc/examples/example_*/

Expand Down
1 change: 1 addition & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -200,3 +200,4 @@ venv/*
.coverage
tests/sciml/models/*
amici_models
doc/examples/example_petab_sciml/Dandekar_Patterns2020/
248 changes: 248 additions & 0 deletions doc/examples/example_petab_sciml/ExamplePEtabSciML.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

1 change: 1 addition & 0 deletions doc/python_examples.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,4 +19,5 @@ Various example notebooks.
examples/example_large_models/example_performance_optimization.ipynb
examples/example_jax/ExampleJax.ipynb
examples/example_jax_petab/ExampleJaxPEtab.ipynb
examples/example_petab_sciml/ExamplePEtabSciML.ipynb
examples/example_splines/ExampleSplines.ipynb
Loading