Release v0.5.5

Merge pull request #1545 from ICB-DCM/develop

.github/CODEOWNERS

@@ -42,6 +42,7 @@
 /pypesto/select/ @dilpath
 /pypesto/startpoint/ @PaulJonasJost
 /pypesto/store/ @PaulJonasJost
+/pypesto/visualize/ @stephanmg
 
 # Tests
 /test/base/ @PaulJonasJost @vwiela

.github/workflows/ci.yml

@@ -55,10 +55,10 @@ jobs:
         CXX: clang++
 
     - name: Coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   mac:
     runs-on: macos-13  # TODO: change to macos-latest after the next release
@@ -91,10 +91,10 @@ jobs:
       run: ulimit -n 65536 65536 && tox -e base
 
     - name: Coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   windows:
     runs-on: windows-latest
@@ -157,16 +157,16 @@ jobs:
 
     - name: Run tests
       timeout-minutes: 35
-      run: tox -e petab
+      run: tox -e petab && tox e -e petab -- pip uninstall -y amici
       env:
         CC: clang
         CXX: clang++
 
     - name: Coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   julia:
     runs-on: ubuntu-latest
@@ -214,10 +214,10 @@ jobs:
       run: tox -e julia
 
     - name: Coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   optimize:
     runs-on: ubuntu-latest
@@ -250,10 +250,10 @@ jobs:
       run: tox -e optimize
 
     - name: Coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   hierarchical:
     runs-on: ubuntu-latest
@@ -286,10 +286,10 @@ jobs:
       run: tox -e hierarchical
 
     - name: Coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   select:
     runs-on: ubuntu-latest
@@ -322,10 +322,10 @@ jobs:
       run: tox -e select
 
     - name: Coverage
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+        files: ./coverage.xml
 
   quality:
     runs-on: ubuntu-latest

.github/workflows/publish_dockerhub.yml

@@ -0,0 +1,32 @@
+name: Build and Push Docker Image
+
+on:
+  push:
+    branches:
+      - develop
+    paths:
+      - 'docker/**'
+      - '.github/workflows/docker-publish.yml'
+  workflow_dispatch:
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_TOKEN }}
+
+      - name: Build and tag the Docker image
+        run: |
+          docker build -t stephanmg/pypesto:latest -f docker/Dockerfile .
+
+      - name: Push the Docker image to Docker Hub
+        run: |
+          docker push stephanmg/pypesto:latest

CHANGELOG.rst

@@ -6,6 +6,56 @@ Release notes
 ..........
 
 
+0.5.5 (2025-01-10)
+-------------------
+
+- **Breaking Changes**
+  - **PETab select**: There are some deprecated features that will show up as warnings. In addition:
+
+    - The plotting methods ignore some arguments. You will need to reimplement these with the newer approach, which uses
+      plotting methods from the PEtab Select library instead. See the model selection notebook for examples.
+
+    - All objects containing multiple models (e.g., dictionaries or lists) are now replaced by `petab_select.Models`,
+      which supports dictionary and list methods.
+
+      To convert your old list of models:
+
+      ```python
+      petab_select.Models(list_of_Model)
+      ```
+- General
+    - Exclude nlopt==2.9.0 from setup (#1519)
+    - Improve CI (#1521, #1523, #1532, #1536, #1508, #1544, #1531)
+    - Update references/documentation (#1506, #1491, #1516, #1543)
+    - **Docker Image** (#1083, #1538)
+- Hierarchical
+    - Fix no error if inner observable parameter in noise formula & viceversa (#1504)
+    - Remove inner datas from relative calculator (#1505)
+    - Fix not scaling inner pars when applying to rdatas (#1534)
+- Optimization
+    - ESSOptimizer: Fix priority for local search startpoints (#1503)
+    - Fix NLoptOptimizer.__repr__ (#1518)
+    - Improve exception-handling in SacessOptimizer (#1517)
+    - Fix ESSOptimizer min of empty sequence (#1510)
+    - Don't modify sys.path for amici model imports (#1522)
+    - Set OptimizerResult.optimizer in Optimizer.minimize (#1525)
+    - SacessOptimizer: More efficient saving of intermediate results (#1529)
+- Objective
+    - AmiciObjective/PEtab import: Fix plist (#1493)
+    - PEtab: Fix warning from fill_in_parameters with fixed parameters (#1509)
+    - Amici: Fix handling of PEtab fixed parameters (#1514)
+    - Fix get_parameter_prior_dict docstring (#1537)
+- Select
+    - Support user-provided calibration results (#1338)
+    - Problem-specific minimize method for SaCeSS (#1339)
+    - Update for the latest PEtab Select version; see example notebook or the PEtab Select repo (#1530)
+- Storage
+    - Enable writing Optimize(r)Result directly in Writer (#1528)
+    - Update parameter scale storage (#1542
+- Visualize
+    - Fix flatten of observable mapping with one observable (#1515)
+
+
 0.5.4 (2024-10-19)
 -------------------