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Merged
sebapersson merged 4 commits into from
May 21, 2026
Merged

Update GitHub workflows #78

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3087396
Test on MacOS and Windows in addition to Linux
sebapersson May 20, 2026
b051bac
Add codecov
sebapersson May 20, 2026
30a2133
Add pytest-cov
sebapersson May 20, 2026
3a66942
Add README badges
sebapersson May 20, 2026
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22 changes: 19 additions & 3 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,20 @@ name: Tests
on:
push:
branches:
- main
- main
pull_request:

jobs:
test:
runs-on: ubuntu-latest
runs-on: ${{ matrix.os }}

strategy:
fail-fast: false
matrix:
os:
- ubuntu-latest
- macos-latest
- windows-latest

steps:
- name: Check out repository
Expand All @@ -28,4 +36,12 @@ jobs:

- name: Run tests
run: |
python -m pytest
python -m pytest --cov=petab_sciml --cov-report=xml --cov-report=term-missing

- name: Coverage
uses: codecov/codecov-action@v6
with:
token: ${{ secrets.CODECOV_TOKEN }}
files: ./coverage.xml
if: matrix.os == 'ubuntu-latest'

5 changes: 4 additions & 1 deletion README.md
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@@ -1,12 +1,15 @@
# PEtab SciML
*A data format for scientific machine learning*

[![Build Status](https://github.com/PEtab-dev/petab_sciml/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/PEtab-dev/petab_sciml/actions/workflows/ci.yml?query=branch%3Amain)
[![codecov](https://codecov.io/gh/PEtab-dev/petab_sciml/graph/badge.svg?token=ki1YcdIHII)](https://codecov.io/gh/PEtab-dev/petab_sciml)

PEtab SciML is a table-based data format for creating training (parameter estimation)
problems for **scientific machine learning (SciML)** models that combine machine learning
and mechanistic ordinary differential equation (ODE) models.

> [!WARNING]
> **Beta Disclaimer**: this software is under active development and may contain bugs or instabilities. The PEtab SciML format is finalised and support for it has been implemented in PEtab importers, though not yet released. Documentation and utility functions are currently being added.
> **Beta Disclaimer**: this software is under active development and may contain bugs or instabilities. The PEtab SciML format is finalised and support for it has been implemented in PEtab importers, though not yet released. Documentation and utility functions are currently being added.

## Highlights

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1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -48,6 +48,7 @@ doc = [
]
test = [
"pytest",
"pytest-cov",
"torch"
]
torch = [
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