Merge pull request #2433 from dweindl/release_0.25.0

Release 0.25.0

Author: dweindl

.git-blame-ignore-revs

@@ -0,0 +1 @@
+f59fed72eb4d0cedf6abf2a96fe95087ce61478a

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]

.github/workflows/deploy_branch.yml

@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/deploy_protected.yml

@@ -29,14 +29,14 @@ jobs:
           fi
 
   dockerhub:
-    name: Deploy Dockerhub
+    name: Deploy Docker Hub
     needs: [check-secret]
     if: needs.check-secret.outputs.secrets-defined == 'true'
     runs-on: ubuntu-22.04
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -50,7 +50,7 @@ jobs:
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v3
     - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@v4
+      uses: elgohr/Publish-Docker-Github-Action@v5
       with:
         name: dweindl/amici
         username: ${{ secrets.DOCKER_USERNAME }}

.github/workflows/deploy_release.yml

@@ -12,7 +12,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     environment:
       name: pypi
@@ -39,7 +39,7 @@ jobs:
     - name: Remove direct dependencies from setup.cfg
       # Remove any "git+https"-based dependencies that are not supported
       #  by PyPI and are only required for testing.
-      run: sed -i '/git+https/d' python/sdist/setup.cfg
+      run: sed -i '/git+https/d' python/sdist/pyproject.toml
 
     - name: sdist
       run: scripts/buildSdist.sh
@@ -74,3 +74,29 @@ jobs:
             -H "Accept: application/vnd.github.v3+json" \
               https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
             -d "{\"ref\": \"dev\", \"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"
+
+  dockerhub:
+    name: Release to Docker Hub
+    runs-on: ubuntu-22.04
+
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+    - uses: actions/checkout@v4
+    - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v3
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    - name: Publish to Registry
+      uses: elgohr/Publish-Docker-Github-Action@v5
+      with:
+        name: dweindl/amici
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        workdir: container/
+        dockerfile: Dockerfile
+        tag_semver: true
+        platforms: linux/amd64,linux/arm64

.github/workflows/test_benchmark_collection_models.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
         extract_subexpressions: ["true", "false"]
     env:
       AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}

.github/workflows/test_doc.yml

@@ -20,7 +20,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_install.yml

@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -50,7 +50,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -83,7 +83,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_performance.yml

@@ -23,7 +23,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_petab_test_suite.yml

@@ -22,7 +22,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}