Merge branch 'develop' into jax_sciml

Author: FFroehlich

.github/workflows/deploy_branch.yml

@@ -5,7 +5,7 @@ jobs:
   sdist:
     name: Deploy Python Source Distribution
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/deploy_protected.yml

@@ -32,7 +32,7 @@ jobs:
     name: Deploy Docker Hub
     needs: [check-secret]
     if: needs.check-secret.outputs.secrets-defined == 'true'
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/deploy_release.yml

@@ -8,7 +8,7 @@ jobs:
   pypi:
     name: Deploy PyPI
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
@@ -47,7 +47,7 @@ jobs:
   bioSimulatorsUpdateCliAndDockerImage:
     name: Release to BioSimulators
     needs: pypi
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     env:
       # Owner/repository-id for the GitHub repository for the downstream command-line interface and Docker image
       DOWNSTREAM_REPOSITORY: biosimulators/Biosimulators_AMICI
@@ -72,7 +72,7 @@ jobs:
 
   dockerhub:
     name: Release to Docker Hub
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
     - name: Set up Python

.github/workflows/test_benchmark_collection_models.yml

@@ -17,7 +17,7 @@ jobs:
   build:
     name: Benchmark Collection
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       fail-fast: false
@@ -77,7 +77,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: coverage_py.xml
+        files: coverage_py.xml
         flags: python
         fail_ci_if_error: true
         verbose: true

.github/workflows/test_doc.yml

@@ -39,7 +39,7 @@ jobs:
 
   sphinx:
     name: Test Sphinx
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/test_install.yml

@@ -5,7 +5,7 @@ jobs:
   archive:
     name: Archive Install
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
@@ -46,7 +46,7 @@ jobs:
   sdist_ubuntu:
     name: sdist Install Ubuntu
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/test_matlab.yml

@@ -12,7 +12,7 @@ jobs:
   matlab:
     name: Matlab
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/test_performance.yml

@@ -19,7 +19,7 @@ jobs:
   build:
     name: Performance Test
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:

.github/workflows/test_petab_test_suite.yml

@@ -104,6 +104,6 @@ jobs:
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          file: coverage.xml
+          files: coverage.xml
           flags: petab
           fail_ci_if_error: true

.github/workflows/test_pypi.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
-        os: [ubuntu-22.04, macos-latest]
+        os: [ubuntu-24.04, macos-latest]
 
     runs-on: ${{ matrix.os }}