Merge pull request #1342 from ICB-DCM/develop

Release v0.5.0

.git-blame-ignore-revs

@@ -0,0 +1,8 @@
+# .git-blame-ignore-revs
+# https://github.com/ICB-DCM/pyPESTO/pull/1352
+321ee9dbd0223da0c08172fc08d61796e0d176aa
+# Adjusted to ruff code-checks. Timestamp: 05.03.2024
+82b7d5da1273b9d442a634e5aabbda9685279d77
+# Adjusted to black formatting. Timestamp: 11.01.2022
+ea0b0b47a2990806a8b8f1f9fa3b4257828e8df9
+165e5f9d36fc7ccc882c14f35ba345b3b6b41c6d

.github/workflows/deploy.yml

@@ -27,8 +27,8 @@ jobs:
 
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
       run: |
         python setup.py sdist bdist_wheel
         twine upload dist/*

.pre-commit-config.yaml

@@ -10,29 +10,6 @@
 # `pre-commit run --all-files` as by default only changed files are checked
 
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.1.0
-  hooks:
-  - id: black
-    description: The uncompromising code formatter
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    name: isort (python)
-  - id: isort
-    name: isort (cython)
-    types: [cython]
-  - id: isort
-    name: isort (pyi)
-    types: [pyi]
-- repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.6.3
-  hooks:
-  - id: nbqa-black
-  - id: nbqa-pyupgrade
-    args: [--py36-plus]
-  - id: nbqa-isort
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -54,12 +31,19 @@ repos:
     description: Replace or check mixed line endings
   - id: trailing-whitespace
     description: Trim trailing whitespaces
-- repo: local
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.11
   hooks:
-  - id: style
-    name: Check style
-    description: Check style
-    pass_filenames: false
-    entry: tox -e project,flake8
-    language: system
-    types: [python]
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - pyproject.toml

CHANGELOG.rst

@@ -2,6 +2,46 @@ Release notes
 =============
 
 
+0.5 series
+..........
+
+
+0.5.0 (2024-04-10)
+-------------------
+
+* General
+    * Include pymc in the documentation. (#1305)
+    * Ruff Codechecks (#1307)
+    * Support RoadRunner as simulator for PEtab problems (#1336, #1347, #1348, #1363)
+* Hierarchical
+   * Semiquant: Fix spline knot initialization (#1313, #1323)
+   * Semiquant: Add spline knots to the optimization result (#1314)
+   * Semiquant: fix inner opt tolerance (#1330)
+   * Relative: Fix return of relative calculator if sim fails (#1315)
+   * Relative: Hierarchical optimization: fix unnecessary simulation (#1327)
+   * Relative: Fix return of inner parameters on objective call (#1333)
+* Optimize
+   * Support ipopt with gradient approximation (#1310)
+   * Deprecate CmaesOptimizer in favor of CmaOptimizer (#1311)
+   * ESSOptimizer: Respect local_n2 in case of failed initial local search (#1328)
+   * Remove CESSOptimizer (#1320)
+   * SacessOptimizer: use 'spawn' start method for multiprocessing (#1353)
+* PEtab
+   * Fix unwanted amici model recompilation in PEtab importer (#1319)
+* Sample
+   * Adding Thermodynamic Integration (#1326, #1361)
+   * Dynesty warnings added (#1324)
+   * Dynesty: method to save raw results (#1331)
+* Ensembles
+   * Ensembles: don't expect OptimizerResult.id to be convertible to `int` (#1351)
+* Misc
+   * Updated Code to match dependency updates (#1316, #1344, #1346, #1345)
+   * Ignore code formatting in git blame (#1317)
+   * Updated deployment method (#1341)
+   * add pyupgrade to codechecks (#1352)
+   * Temporarily require scipy<1.13.0 for pypesto[pymc] (#1360)
+
+
 0.4 series
 ..........
 

doc/api.rst

@@ -16,6 +16,7 @@ API reference
    pypesto.objective.aesara
    pypesto.objective.jax
    pypesto.objective.julia
+   pypesto.objective.roadrunner
    pypesto.optimize
    pypesto.petab
    pypesto.predict