Release v0.6.0

Author: PaulJonasJost

.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.13']
+        python-version: ['3.11', '3.14']
 
     steps:
     - name: Check out repository
@@ -64,7 +64,7 @@ jobs:
     runs-on: macos-14
     strategy:
       matrix:
-        python-version: ['3.13']
+        python-version: ['3.14']
 
     steps:
     - name: Check out repository
@@ -100,7 +100,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ['3.13']
+        python-version: ['3.14']
 
     steps:
     - name: Check out repository
@@ -133,7 +133,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.13']
+        python-version: ['3.11', '3.14']
 
     steps:
     - name: Check out repository
@@ -223,7 +223,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.13']
+        python-version: ['3.14']
 
     steps:
     - name: Check out repository
@@ -259,7 +259,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.13']
+        python-version: ['3.11', '3.14']
 
     steps:
     - name: Check out repository
@@ -295,7 +295,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.13']
+        python-version: ['3.11', '3.14']
 
     steps:
     - name: Check out repository
@@ -331,7 +331,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.13']
+        python-version: ['3.14']
 
     steps:
     - name: Check out repository
@@ -363,7 +363,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.13']
 
     steps:
     - name: Check out repository

.github/workflows/deploy.yml

@@ -15,10 +15,10 @@ jobs:
     - name: Check out repository
       uses: actions/checkout@v6
 
-    - name: Remove direct dependencies from setup.cfg
+    - name: Remove direct dependencies from pyproject.toml
       # Remove any "git+https"-based dependencies that are not supported
       #  by PyPI and are only required for testing.
-      run: sed -i '/git+https/d' setup.cfg
+      run: sed -i '/git+https/d' pyproject.toml
 
     - name: Prepare python ${{ matrix.python-version }}
       uses: actions/setup-python@v6

.github/workflows/publish_dockerhub.yml

@@ -18,7 +18,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_TOKEN }}

.readthedocs.yml

@@ -26,4 +26,4 @@ build:
     - libhdf5-serial-dev
     - swig
   tools:
-    python: "3.11"
+    python: "3.13"

CHANGELOG.rst

@@ -1,6 +1,56 @@
 Release notes
 =============
 
+Versioning
+..........
+
+pyPESTO follows `EffVer <https://jacobtomlinson.dev/effver/>`_ (Intended Effort Versioning).
+Version numbers communicate the expected effort required for users to adopt a new release:
+
+- **Macro (X.0.0)**: Significant effort required. Major breaking changes or feature overhauls.
+  You will need to dedicate significant time to upgrade.
+- **Meso (0.X.0)**: Moderate effort required. Small breaking changes, dependency updates,
+  or bug fixes you may have worked around. Some adjustments may be needed.
+- **Micro (0.0.X)**: Minimal effort required. Bug fixes and new orthogonal features.
+  You shouldn't need to change anything.
+
+**Deprecation Policy:**
+
+Breaking changes follow a staged deprecation process to give users time to adapt:
+
+1. **Meso release N**: Feature marked as deprecated with ``DeprecationWarning``.
+   Old functionality still works, but warnings inform users of upcoming changes.
+2. **Meso release N+1** (or later): Deprecated feature is removed or breaking change is applied.
+   This change is clearly documented in the release notes under "Breaking Changes."
+
+This policy ensures users have at least one full Meso release cycle to adapt their code
+before breaking changes take effect.
+
+
+0.6 series
+..........
+
+
+0.6.0 (2026-03-13)
+------------------
+
+- General
+    - Support for Python 3.14 (#1620)
+- Optimization
+    - Make `id` optional in `Optimizer.minimize` (#1692)
+- Visualize
+    - Make parameters_correlation_matrix more customizable (#1695)
+- Documentation
+    - More readable figures in examples (#1691)
+- Installation / Packaging
+    - Require amici>=1.0.0 (#1619)
+- Performance
+    - Change from Pool to ProcessPoolExecutor (#1664)
+- Bugfixes
+    - Make validate_inner_parameter_pairings pandas 3 compatible (#1696)
+- Deprecations
+    - Add deprecation warning in SacessOptimizer and ESSOptimizer (#1690)
+
 
 0.5 series
 ..........

doc/conf.py

@@ -102,6 +102,7 @@
     "petab_select": ("https://petab-select.readthedocs.io/en/develop/", None),
     "python": ("https://docs.python.org/3", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "seaborn": ("https://seaborn.pydata.org/", None),
 }
 
 

doc/example.rst

@@ -67,3 +67,4 @@ Application examples
 
    example/conversion_reaction.ipynb
    example/synthetic_data.ipynb
+   example/example_amici_splines_swameye/example_amici_splines_Swameye2003.ipynb