From 3087396d558ff0fefd0e69c274bd7ded64c7eb6a Mon Sep 17 00:00:00 2001 From: sebapersson Date: Wed, 20 May 2026 16:07:16 +0100 Subject: [PATCH 1/4] Test on MacOS and Windows in addition to Linux --- .github/workflows/ci.yml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b7e8abc..b8af2dc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -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 From b051bac83b2052d8f520f2dcff6e3a432fa0fb0b Mon Sep 17 00:00:00 2001 From: sebapersson Date: Wed, 20 May 2026 16:25:39 +0100 Subject: [PATCH 2/4] Add codecov --- .github/workflows/ci.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b8af2dc..28e1f3c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -36,4 +36,11 @@ jobs: - name: Run tests run: | - python -m pytest \ No newline at end of file + 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 }} + if: matrix.os == 'ubuntu-latest' + \ No newline at end of file From 30a2133313d0a7e18a4f37c7dd29d07fe186fb9c Mon Sep 17 00:00:00 2001 From: sebapersson Date: Wed, 20 May 2026 16:32:22 +0100 Subject: [PATCH 3/4] Add pytest-cov --- .github/workflows/ci.yml | 1 + pyproject.toml | 1 + 2 files changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 28e1f3c..8298978 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -42,5 +42,6 @@ jobs: uses: codecov/codecov-action@v6 with: token: ${{ secrets.CODECOV_TOKEN }} + files: ./coverage.xml if: matrix.os == 'ubuntu-latest' \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 0ee94ac..cad7f4a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,6 +48,7 @@ doc = [ ] test = [ "pytest", + "pytest-cov", "torch" ] torch = [ From 3a669426203d7562039892d0068f98decb896492 Mon Sep 17 00:00:00 2001 From: sebapersson Date: Wed, 20 May 2026 16:51:13 +0100 Subject: [PATCH 4/4] Add README badges --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4f2d43f..9ad8fc0 100644 --- a/README.md +++ b/README.md @@ -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