Update to python 3.13

Author: bartvanb

.github/workflows/release.yml

@@ -15,7 +15,7 @@ jobs:
             - name: Setup Python
               uses: actions/setup-python@v3
               with:
-                  python-version: "3.10"
+                  python-version: "3.13"
 
             - name: Install dependencies
               run: |

.readthedocs.yml

@@ -4,7 +4,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.13"
   # install R
   apt_packages:
     - r-base

circe/setup.py

@@ -1,38 +1,36 @@
 import codecs
-
-from setuptools import setup, find_namespace_packages
 from pathlib import Path
 
+from setuptools import find_namespace_packages, setup
+
 # get current directory
 here = Path(__file__).parent.absolute()
 parent_dir = here.parent.absolute()
 
 # get the long description from the README file
-with codecs.open(parent_dir / 'README.md', encoding='utf-8') as f:
+with codecs.open(parent_dir / "README.md", encoding="utf-8") as f:
     long_description = f.read()
 
 # get the version from the parent dir
-with open(parent_dir / 'VERSION') as f:
+with open(parent_dir / "VERSION") as f:
     version = f.read().strip()
 
 # setup the package
 setup(
-    name='ohdsi-circe',
+    name="ohdsi-circe",
     version=version,
-    description='Python wrapper for the OHDSI R packages',
+    description="Python wrapper for the OHDSI R packages",
     long_description=long_description,
-    long_description_content_type='text/markdown',
-    url='https://github.com/vantage6/python-ohdsi',
-    packages=find_namespace_packages(include=['ohdsi.*']),
-    python_requires='>=3.10',
+    long_description_content_type="text/markdown",
+    url="https://github.com/vantage6/python-ohdsi",
+    packages=find_namespace_packages(include=["ohdsi.*"]),
+    python_requires=">=3.13",
     install_requires=[
-        'rpy2==3.5.12',
+        "rpy2==3.5.12",
     ],
-    extras_require={
-        'dev': []
-    },
+    extras_require={"dev": []},
     package_data={
-        'ohdsi.circe.data': ['*.json'],
+        "ohdsi.circe.data": ["*.json"],
     },
     # entry_points={
     #     'console_scripts': [

cohort-diagnostics/setup.py

@@ -1,39 +1,37 @@
 import codecs
-
-from setuptools import setup, find_namespace_packages
 from pathlib import Path
 
+from setuptools import find_namespace_packages, setup
+
 # get current directory
 here = Path(__file__).parent.absolute()
 parent_dir = here.parent.absolute()
 
 # get the long description from the README file
-with codecs.open(parent_dir / 'README.md', encoding='utf-8') as f:
+with codecs.open(parent_dir / "README.md", encoding="utf-8") as f:
     long_description = f.read()
 
 # get the version from the parent dir
-with open(parent_dir / 'VERSION') as f:
+with open(parent_dir / "VERSION") as f:
     version = f.read().strip()
 
 # setup the package
 setup(
-    name='ohdsi-cohort-diagnostics',
+    name="ohdsi-cohort-diagnostics",
     version=version,
-    description='Python wrapper for the OHDSI R packages',
+    description="Python wrapper for the OHDSI R packages",
     long_description=long_description,
-    long_description_content_type='text/markdown',
-    url='https://github.com/vantage6/python-ohdsi',
-    packages=find_namespace_packages(include=['ohdsi.*']),
-    python_requires='>=3.10',
+    long_description_content_type="text/markdown",
+    url="https://github.com/vantage6/python-ohdsi",
+    packages=find_namespace_packages(include=["ohdsi.*"]),
+    python_requires=">=3.13",
     install_requires=[
-        'rpy2==3.5.12',
-        'pandas==2.3.1',
+        "rpy2==3.5.12",
+        "pandas==2.3.1",
     ],
-    extras_require={
-        'dev': []
-    },
+    extras_require={"dev": []},
     package_data={
-        'ohdsi.cohort_diagnostics.data': ['*.json'],
+        "ohdsi.cohort_diagnostics.data": ["*.json"],
     },
     # entry_points={
     #     'console_scripts': [

cohort-generator/setup.py

@@ -1,40 +1,36 @@
 import codecs
-
-from setuptools import setup, find_namespace_packages
 from pathlib import Path
 
+from setuptools import find_namespace_packages, setup
+
 # get current directory
 here = Path(__file__).parent.absolute()
 parent_dir = here.parent.absolute()
 
 # get the long description from the README file
-with codecs.open(parent_dir / 'README.md', encoding='utf-8') as f:
+with codecs.open(parent_dir / "README.md", encoding="utf-8") as f:
     long_description = f.read()
 
 # get the version from the parent dir
-with open(parent_dir / 'VERSION') as f:
+with open(parent_dir / "VERSION") as f:
     version = f.read().strip()
 
 # setup the package
 setup(
-    name='ohdsi-cohort-generator',
+    name="ohdsi-cohort-generator",
     version=version,
-    description='Python wrapper for the OHDSI R packages',
+    description="Python wrapper for the OHDSI R packages",
     long_description=long_description,
-    long_description_content_type='text/markdown',
-    url='https://github.com/vantage6/python-ohdsi',
-    packages=find_namespace_packages(include=['ohdsi.*']),
-    python_requires='>=3.10',
+    long_description_content_type="text/markdown",
+    url="https://github.com/vantage6/python-ohdsi",
+    packages=find_namespace_packages(include=["ohdsi.*"]),
+    python_requires=">=3.13",
     install_requires=[
-        'rpy2==3.5.12',
+        "rpy2==3.5.12",
     ],
-    extras_require={
-        'dev': []
-    },
+    extras_require={"dev": []},
     package_data={
-        'ohdsi.cohort_generator.cohorts': [
-            'data/cohort/*'
-        ],
+        "ohdsi.cohort_generator.cohorts": ["data/cohort/*"],
     },
     # entry_points={
     #     'console_scripts': [

common/setup.py

@@ -1,39 +1,37 @@
 import codecs
-
-from setuptools import setup, find_namespace_packages
 from pathlib import Path
 
+from setuptools import find_namespace_packages, setup
+
 # get current directory
 here = Path(__file__).parent.absolute()
 parent_dir = here.parent.absolute()
 
 # get the long description from the README file
-with codecs.open(parent_dir / 'README.md', encoding='utf-8') as f:
+with codecs.open(parent_dir / "README.md", encoding="utf-8") as f:
     long_description = f.read()
 
 # get the version from the parent dir
-with open(parent_dir / 'VERSION') as f:
+with open(parent_dir / "VERSION") as f:
     version = f.read().strip()
 
 # setup the package
 setup(
-    name='ohdsi-common',
+    name="ohdsi-common",
     version=version,
-    description='Python wrapper for the OHDSI R packages',
+    description="Python wrapper for the OHDSI R packages",
     long_description=long_description,
-    long_description_content_type='text/markdown',
-    url='https://github.com/vantage6/python-ohdsi',
-    packages=find_namespace_packages(include=['ohdsi.*']),
-    python_requires='>=3.10',
+    long_description_content_type="text/markdown",
+    url="https://github.com/vantage6/python-ohdsi",
+    packages=find_namespace_packages(include=["ohdsi.*"]),
+    python_requires=">=3.13",
     install_requires=[
-        'rpy2==3.5.12',
-        'pandas==2.3.1',
+        "rpy2==3.5.12",
+        "pandas==2.3.1",
     ],
-    extras_require={
-        'dev': []
-    },
+    extras_require={"dev": []},
     package_data={
-        'ohdsi.database_connector.java': ['*.jar'],
+        "ohdsi.database_connector.java": ["*.jar"],
     },
     # entry_points={
     #     'console_scripts': [

database-connector/setup.py

@@ -1,38 +1,36 @@
 import codecs
-
-from setuptools import setup, find_namespace_packages
 from pathlib import Path
 
+from setuptools import find_namespace_packages, setup
+
 # get current directory
 here = Path(__file__).parent.absolute()
 parent_dir = here.parent.absolute()
 
 # get the long description from the README file
-with codecs.open(parent_dir / 'README.md', encoding='utf-8') as f:
+with codecs.open(parent_dir / "README.md", encoding="utf-8") as f:
     long_description = f.read()
 
 # get the version from the parent dir
-with open(parent_dir / 'VERSION') as f:
+with open(parent_dir / "VERSION") as f:
     version = f.read().strip()
 
 # setup the package
 setup(
-    name='ohdsi-database-connector',
+    name="ohdsi-database-connector",
     version=version,
-    description='Python wrapper for the OHDSI R packages',
+    description="Python wrapper for the OHDSI R packages",
     long_description=long_description,
-    long_description_content_type='text/markdown',
-    url='https://github.com/vantage6/python-ohdsi',
-    packages=find_namespace_packages(include=['ohdsi.*']),
-    python_requires='>=3.10',
+    long_description_content_type="text/markdown",
+    url="https://github.com/vantage6/python-ohdsi",
+    packages=find_namespace_packages(include=["ohdsi.*"]),
+    python_requires=">=3.13",
     install_requires=[
-        'rpy2==3.5.12',
+        "rpy2==3.5.12",
     ],
-    extras_require={
-        'dev': []
-    },
+    extras_require={"dev": []},
     package_data={
-        'ohdsi.database_connector.java': ['*.jar'],
+        "ohdsi.database_connector.java": ["*.jar"],
     },
     # entry_points={
     #     'console_scripts': [

feature-extraction/setup.py

@@ -1,36 +1,34 @@
 import codecs
-
-from setuptools import setup, find_namespace_packages
 from pathlib import Path
 
+from setuptools import find_namespace_packages, setup
+
 # get current directory
 here = Path(__file__).parent.absolute()
 parent_dir = here.parent.absolute()
 
 # get the long description from the README file
-with codecs.open(parent_dir / 'README.md', encoding='utf-8') as f:
+with codecs.open(parent_dir / "README.md", encoding="utf-8") as f:
     long_description = f.read()
 
 # get the version from the parent dir
-with open(parent_dir / 'VERSION') as f:
+with open(parent_dir / "VERSION") as f:
     version = f.read().strip()
 
 # setup the package
 setup(
-    name='ohdsi-feature-extraction',
+    name="ohdsi-feature-extraction",
     version=version,
-    description='Python wrapper for the OHDSI R packages',
+    description="Python wrapper for the OHDSI R packages",
     long_description=long_description,
-    long_description_content_type='text/markdown',
-    url='https://github.com/vantage6/python-ohdsi',
-    packages=find_namespace_packages(include=['ohdsi.*']),
-    python_requires='>=3.10',
+    long_description_content_type="text/markdown",
+    url="https://github.com/vantage6/python-ohdsi",
+    packages=find_namespace_packages(include=["ohdsi.*"]),
+    python_requires=">=3.13",
     install_requires=[
-        'rpy2==3.5.12',
+        "rpy2==3.5.12",
     ],
-    extras_require={
-        'dev': []
-    },
+    extras_require={"dev": []},
     package_data={
         # 'ohdsi.feature_extraction.data': ['*.json'],
     },

sqlrender/setup.py

@@ -1,39 +1,37 @@
 import codecs
-
-from setuptools import setup, find_namespace_packages
 from pathlib import Path
 
+from setuptools import find_namespace_packages, setup
+
 # get current directory
 here = Path(__file__).parent.absolute()
 parent_dir = here.parent.absolute()
 
 # get the long description from the README file
-with codecs.open(parent_dir / 'README.md', encoding='utf-8') as f:
+with codecs.open(parent_dir / "README.md", encoding="utf-8") as f:
     long_description = f.read()
 
 # get the version from the parent dir
-with open(parent_dir / 'VERSION') as f:
+with open(parent_dir / "VERSION") as f:
     version = f.read().strip()
 
 # setup the package
 setup(
-    name='ohdsi-sqlrender',
+    name="ohdsi-sqlrender",
     version=version,
-    description='Python wrapper for the OHDSI R packages',
+    description="Python wrapper for the OHDSI R packages",
     long_description=long_description,
-    long_description_content_type='text/markdown',
-    url='https://github.com/vantage6/python-ohdsi',
-    packages=find_namespace_packages(include=['ohdsi.*']),
-    python_requires='>=3.10',
+    long_description_content_type="text/markdown",
+    url="https://github.com/vantage6/python-ohdsi",
+    packages=find_namespace_packages(include=["ohdsi.*"]),
+    python_requires=">=3.13",
     install_requires=[
-        'rpy2==3.5.12',
-        'pandas==2.3.1',
+        "rpy2==3.5.12",
+        "pandas==2.3.1",
     ],
-    extras_require={
-        'dev': []
-    },
+    extras_require={"dev": []},
     package_data={
-        'ohdsi.sqlrender.data': ['*.json'],
+        "ohdsi.sqlrender.data": ["*.json"],
     },
     # entry_points={
     #     'console_scripts': [