Merge branch 'develop' into doc_all

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]
+    target-branch: "develop"

.github/workflows/ci.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:
         # test on latest and minimum python version
-        python-version: ['3.11', '3.9']
+        python-version: ['3.12', '3.10']
 
     steps:
     - name: Check out repository

.github/workflows/deploy_release.yml

@@ -0,0 +1,34 @@
+name: Deploy
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  pypi:
+    name: Deploy PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/petab-select
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 20
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel build
+        python -m build -s
+
+    - name: Publish a Python distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -1,5 +1,7 @@
 # PEtab Select
 
+[![PyPI - Version](https://img.shields.io/pypi/v/petab-select)](https://pypi.org/project/petab-select/)
+
 The repository for the development of the extension to PEtab for model
 selection, including the additional file formats and Python 3 package.
 

doc/examples/workflow_cli.ipynb

@@ -47,7 +47,7 @@
    "source": [
     "In each call to `petab_select search`, the following options are required:\n",
     "- `-y`: The PEtab Select problem YAML file;\n",
-    "- `-s`: A file that is used to stored the state of the problem (e.g., such that models are not repeated);\n",
+    "- `-s`: A file that is used to store the state of the problem (e.g., such that models are not repeated);\n",
     "- `-o`: A file to store the output of the model space search; and\n",
     "- `-m`: The method used to search or identify models in the model space.\n",
     "\n",
@@ -570,7 +570,7 @@
    "id": "655f8efc",
    "metadata": {},
    "source": [
-    "# Post-processing\n",
+    "## Post-processing\n",
     "After the selection algorithm has terminated, the best model can be stored separately by supplying a list of calibrated models."
    ]
   },

petab_select/criteria.py

@@ -1,8 +1,8 @@
 """Implementations of model selection criteria."""
 
 import numpy as np
-import petab
-from petab.C import OBJECTIVE_PRIOR_PARAMETERS, OBJECTIVE_PRIOR_TYPE
+import petab.v1 as petab
+from petab.v1.C import OBJECTIVE_PRIOR_PARAMETERS, OBJECTIVE_PRIOR_TYPE
 
 import petab_select
 

petab_select/model.py

@@ -5,10 +5,10 @@
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
 
-import petab
+import petab.v1 as petab
 import yaml
 from more_itertools import one
-from petab.C import ESTIMATE, NOMINAL_VALUE
+from petab.v1.C import ESTIMATE, NOMINAL_VALUE
 
 from .constants import (
     CRITERIA,

petab_select/petab.py

@@ -1,9 +1,9 @@
 from pathlib import Path
 from typing import List, Optional
 
-import petab
+import petab.v1 as petab
 from more_itertools import one
-from petab.C import ESTIMATE, NOMINAL_VALUE
+from petab.v1.C import ESTIMATE, NOMINAL_VALUE
 
 from .constants import PETAB_ESTIMATE_FALSE, TYPE_PARAMETER_DICT, TYPE_PATH
 

petab_select/ui.py

@@ -3,7 +3,7 @@
 from typing import Dict, List, Optional, Union
 
 import numpy as np
-import petab
+import petab.v1 as petab
 
 from .candidate_space import CandidateSpace, FamosCandidateSpace
 from .constants import (

setup.py

@@ -30,8 +30,7 @@ def absolute_links(txt):
     return txt
 
 
-# 3.7.1 for NumPy, 3.8 for `typing.get_args`
-minimum_python_version = '3.8'
+minimum_python_version = '3.10'
 if sys.version_info < tuple(map(int, minimum_python_version.split('.'))):
     sys.exit(f'PEtab Select requires Python >= {minimum_python_version}')