feat: python 3.13 support

Co-authored-by: mfranczel <mfranczel@users.noreply.github.com>

Author: FilipPyrek

.cursorrules

@@ -137,6 +137,7 @@ Supported versions:
 - Python 3.10
 - Python 3.11
 - Python 3.12
+- Python 3.13
 
 ## Code Examples
 

.github/workflows/cd.yml

@@ -35,7 +35,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.9", "3.10", "3.11", "3.12"]
+        python_version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     permissions:
       id-token: write
       contents: read
@@ -413,7 +413,7 @@ jobs:
     needs: build-and-push-artifacts-status
     if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/')
     env:
-      PYTHON_VERSIONS: "3.9,3.10,3.11,3.12"
+      PYTHON_VERSIONS: "3.9,3.10,3.11,3.12,3.13"
     steps:
       - name: Checkout code
         uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955 # v4

.github/workflows/ci.yml

@@ -162,7 +162,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - name: Checkout code
@@ -283,7 +283,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - name: Checkout code
         uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955 # v4
@@ -299,11 +299,11 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Set up Java 11
+      - name: Set up Java 17
         uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
         with:
           distribution: 'temurin'
-          java-version: '11'
+          java-version: '17'
 
       - name: Load cached Poetry installation
         id: cached-poetry

.mise.toml

@@ -4,7 +4,7 @@
 
 [tools]
 python = "3.12"
-java = "temurin-11"
+java = "temurin-17"
 poetry = "2.2.0"
 
 [tasks.setup]

CLAUDE.md

@@ -52,7 +52,7 @@
 
 ## Python Version Support
 
-- Python 3.9, 3.10, 3.11, 3.12
+- Python 3.9, 3.10, 3.11, 3.12, 3.13
 
 ## Dependencies
 

README.md

@@ -37,17 +37,17 @@ The toolkit consists of two main bundle types:
 2. Run setup:
 
     ```bash
-    mise install        # Installs Python 3.12 and Java 11
+    mise install        # Installs Python 3.12 and Java 17
     mise run setup      # Installs dependencies and pre-commit hooks
     ```
 
 #### Option 2: Manual setup
 
 1. Install poetry: [Installation](https://python-poetry.org/docs/#installation)
-2. Install Java 11 (required for PySpark tests):
+2. Install Java 17 (required for PySpark tests):
     - macOS: `brew install openjdk@11`
-    - Ubuntu/Debian: `sudo apt-get install openjdk-11-jdk`
-    - RHEL/Fedora: `sudo dnf install java-11-openjdk-devel`
+    - Ubuntu/Debian: `sudo apt-get install openjdk-17-jdk`
+    - RHEL/Fedora: `sudo dnf install java-17-openjdk-devel`
 3. Set up venv for development package:
 
     ```bash
@@ -277,7 +277,7 @@ $ ./bin/test-local
 
 We use Docker to ensure reproducible environments due to Jupyter libraries' binary dependencies:
 
-- `builder.Dockerfile`: Creates Python package bundles for different versions (3.9-3.12), generates kernel and server bundles, and packages the toolkit for distribution using Poetry.
+- `builder.Dockerfile`: Creates Python package bundles for different versions (3.9-3.13), generates kernel and server bundles, and packages the toolkit for distribution using Poetry.
 
 - `test.Dockerfile`: Provides consistent test environment for running unit and integration tests across Python versions using nox. Used both locally and in CI/CD pipeline.
 

deepnote_toolkit/ocelots/pandas/analyze.py

@@ -83,9 +83,15 @@ def _get_histogram(pd_series):
             {"bin_start": bins[i], "bin_end": bins[i + 1], "count": count.item()}
             for i, count in enumerate(y)
         ]
-    except IndexError:
-        # numpy bug https://github.com/numpy/numpy/issues/8627
-        return None
+    except ValueError as e:
+        # NumPy 2.2+ raises "Too many bins for data range" when:
+        # - Data range is zero (all values identical), or
+        # - For integer data, bin width would be < 1.0, or
+        # - Floating point precision prevents creating finite-sized bins at large scales
+        # Numpy implementation: https://github.com/numpy/numpy/blob/e7a123b2d3eca9897843791dd698c1803d9a39c2/numpy/lib/_histograms_impl.py#L454
+        if "Too many bins for data range" in str(e):
+            return None
+        raise
 
 
 def _calculate_min_max(column):

dockerfiles/test.Dockerfile

@@ -2,7 +2,7 @@ FROM quay.io/pypa/manylinux_2_28_x86_64:2025.05.28-1
 RUN pipx install nox poetry==2.2.0
 
 RUN dnf -y update && \
-    dnf -y install java-11-openjdk-devel \
+    dnf -y install java-17-openjdk-devel \
     # Required for pymssql - provides sqlfront.h header file
     freetds-devel \
     # Required for database connectivity through ODBC

noxfile.py

@@ -3,7 +3,7 @@
 from nox import session
 
 
-@session(python=["3.9", "3.10", "3.11", "3.12"], reuse_venv=True)
+@session(python=["3.9", "3.10", "3.11", "3.12", "3.13"], reuse_venv=True)
 def unit(session):
     """Run unit tests. Coverage is disabled by default, use --coverage to enable."""
 
@@ -67,7 +67,7 @@ def unit(session):
     )
 
 
-@session(python=["3.9", "3.10", "3.11", "3.12"], reuse_venv=True)
+@session(python=["3.9", "3.10", "3.11", "3.12", "3.13"], reuse_venv=True)
 def integration(session):
     """Run integration tests. Coverage is disabled by default, use --coverage to enable."""
     # Validate required environment variables

pyproject.toml

@@ -15,7 +15,7 @@ maintainers = [
 ]
 readme = "README.md"
 license = {text = "Apache-2.0"}
-requires-python = ">=3.9.0,<3.13,!=3.9.7"
+requires-python = ">=3.9.0,<3.14,!=3.9.7"
 keywords = [
     "deepnote",
     "jupyter",
@@ -39,6 +39,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Operating System :: OS Independent",
     "Environment :: Console",
     "Framework :: Jupyter"
@@ -47,55 +48,70 @@ dependencies = [
     # Core data libraries
     "pandas>=1.2.5,<2.2; python_version < '3.12'",
     "pandas>=2.1.0,<2.3; python_version >= '3.12'",
+    "pandas>=2.2.3,<2.4; python_version >= '3.13'",
     "numpy>=1.21,<2; python_version >= '3.9' and python_version < '3.10'",
     "numpy>=1.23,<2; python_version >= '3.10' and python_version < '3.11'",
     "numpy>=1.24,<2; python_version >= '3.11' and python_version < '3.12'",
-    "numpy>=1.26.0,<2; python_version >= '3.12'",
+    "numpy>=1.26.0,<2; python_version == '3.12'",
+    "numpy>=2.1.0,<3; python_version >= '3.13'",
 
     # SQL and database dependencies
     "duckdb>=1.1.0,<2.0.0; python_version < '3.12'",
-    "duckdb>=1.1.0; python_version >= '3.12'",
-    "google-cloud-bigquery-storage==2.16.2",
+    "duckdb>=1.1.0,<2.0.0; python_version >= '3.12'",
+    "duckdb>=1.4.1,<2.0.0; python_version >= '3.13'",
+    "google-cloud-bigquery-storage==2.16.2; python_version < '3.13'",
+    "google-cloud-bigquery-storage>=2.33.1,<3; python_version>='3.13'",
 
     "pyarrow>=10.0.0,<=17.0.0; python_version >= '3.9' and python_version < '3.11' and sys_platform != 'darwin'",
     "pyarrow>=16.0.0,<18.0.0; python_version >= '3.9' and python_version < '3.11' and sys_platform == 'darwin'",
     "pyarrow>=13.0.0,<=17.0.0; python_version >= '3.11' and python_version < '3.12' and sys_platform != 'darwin'",
     "pyarrow>=16.0.0,<=18.0.0; python_version >= '3.11' and python_version < '3.12' and sys_platform == 'darwin'",
     "pyarrow>=14.0.1; python_version >= '3.12'",
+    "pyarrow>=18.0.0,<22.0; python_version >= '3.13'",
 
     "db-dtypes>=1.2.0,<1.4",
 
     # pymssql: macOS uses versions with ARM64 wheels (2.3.5+)
     "pymssql>=2.3.5,<2.4; python_version >= '3.9' and sys_platform == 'darwin'",
     "pymssql>=2.2.9,<2.4; python_version >= '3.9' and python_version < '3.12' and sys_platform != 'darwin'",
     "pymssql>=2.3.0,<2.4; python_version >= '3.12' and sys_platform != 'darwin'",
+    "pymssql>=2.3.8,<2.4; python_version >= '3.13'",
 
     "sshtunnel==0.4.0",
     "psycopg2-binary>=2.9.4,<2.9.10; sys_platform == 'darwin' and python_version == '3.9'",
     "psycopg2-binary>=2.9.4,<2.10; sys_platform != 'darwin' or python_version >= '3.10'",
+    "psycopg2-binary>=2.9.10,<3; python_version>='3.13'",
 
     # SQL templating
     "jinja2>=3.1.6,<4",
     "sqlparse>=0.4.4,<0.6",
-    "ipykernel>6.22.0",
+    "ipykernel>6.30.0",
     "pymysql>=1.1.1,<1.2",
-    "pymongo>=4.6.3,<4.10",
-    "dnspython>=2.6.1,<2.7",
+    "pymongo>=4.6.3,<4.10; python_version < '3.13'",
+    "pymongo>=4.9.0,<5; python_version>='3.13'",
+    "dnspython>=2.6.1,<2.7; python_version < '3.13'",
+    "dnspython>=2.7.0,<3.0; python_version>='3.13'",
     "paramiko>=3.4.0,<3.6",
     "sqlalchemy<2; python_version <= '3.11'",
+    "sqlalchemy>=2.0.31,<3; python_version >= '3.13'",
     "snowflake-sqlalchemy>=1.6.0,<1.8",
     "snowflake-connector-python>=3.13.1",
+    "snowflake-connector-python>=3.16.0,<5; python_version>='3.13'",
     "sqlalchemy-spanner>=1.6.2,<2",
     "clickhouse-sqlalchemy>0,<0.4",
-    "sqlalchemy-bigquery>1.6.1,<1.13",
+    "sqlalchemy-bigquery>1.6.1,<1.13; python_version < '3.13'",
+    "sqlalchemy-bigquery>=1.15.0,<1.20; python_version>='3.13'",
     "zstd>1.5.5.1; python_version < '3.11'",
     "zstd>1.5.7.0; python_version >= '3.11' and python_version < '3.12'",
     "zstd>1.5.7.0; python_version >= '3.12'",
     "deepnote-sqlalchemy-redshift==0.8.17",
     "trino[sqlalchemy]>=0.327.0,<=0.330.0",
+    "trino[sqlalchemy]>=0.329.0,<=0.336.0; python_version>='3.13'",
     "pyathena[sqlalchemy]==3.9.0",
+    "pyathena[sqlalchemy]>=3.9.0,<4; python_version>='3.13'",
     "sqlalchemy-dremio>=3.0.3,<3.1",
-    "dill==0.3.8",
+    "dill>=0.3.8,<=0.4; python_version <= '3.12'",
+    "dill>=0.3.9,<=0.4; python_version >= '3.13'",
 
     # AlloyDB
     "pg8000==1.31.5",
@@ -122,9 +138,15 @@ dependencies = [
 
     # Config dependencies - they need to be declared both in main and server extras, keep them in sync
     "pydantic>=1.10.0,<3",
+    "pydantic>=2.8.0,<3; python_version>='3.13'",
     "pyyaml>=6,<7",
     "tomli>=2,<3; python_version < '3.11'",
-    "toml>=0.10.0,<1.0.0"
+    "toml>=0.10.0,<1.0.0",
+    "toml>=0.10.0,<1.0.0",
+
+    # Compatibility constraints for transitive dependencies
+    "grpcio>=1.66.2; python_version >= '3.13'",
+    "greenlet>=3.1.0; python_version >= '3.13'"
 ]
 
 [project.urls]
@@ -143,6 +165,7 @@ server = [
 
     # Config dependencies - they need to be declared both in main and server extras, keep them in sync
     "pydantic>=1.10.0,<3",
+    "pydantic>=2.8.0,<3; python_version>='3.13'",
     "pyyaml>=6,<7",
     "tomli>=2,<3; python_version < '3.11'",
     "toml>=0.10.0,<1.0.0"
@@ -154,24 +177,25 @@ deepnote-toolkit = "deepnote_toolkit.cli.main:main"
 
 [dependency-groups]
 dev = [
-    "pylint>=3.2.5,<4.0.0",
+    "pylint>=3.3.0,<4.0.0",
     "flake8>=7.1.0,<8.0.0",
     "black>=24.4.2,<25.0.0",
     "isort>=5.13.2,<6.0.0",
     "pytest>=8.3.1,<9.0.0",
     "pytest-cov>=6.0.0,<7.0.0",
     "coverage[toml]>=7.10.0,<8.0.0",
-    "mypy>=1.11.0,<2.0.0",
+    "mypy>=1.13.0,<2.0.0",
     "pre-commit>=3.6.0,<4.0.0; python_version >= '3.10'",
     "pre-commit<3.6.0; python_version >= '3.9' and python_version < '3.10'",
-    "responses>=0.25.3,<0.26.0",
+    "responses>=0.25.7,<0.26.0",
     "parameterized>=0.9.0,<0.10.0",
     "geopandas>=0.11.1,<1.1; python_version < '3.12'",
     "geopandas>=0.13.2; python_version >= '3.12'",
     # We do not distribute PySpark for all users because it's huge dependency (300mb) and not all
     # users need it. So in code we get pyspark from global module cache (since user already imported it at
     # that point). But we also have it as dev dependency to provide better autocompletion and for tests
-    "pyspark>=3.5.5,<4.0.0",
+    "pyspark>=3.5.5,<4.0.0; python_version < '3.13'",
+    "pyspark>=4.0.0,<5.0.0; python_version >= '3.13'",
     "nox>=2025.5.1,<2026.0.0",
     "poetry-dynamic-versioning>=1.4.0,<2.0.0",
     "twine>=6.1.0,<7.0.0",
@@ -182,7 +206,8 @@ license-check = [
     # Dependencies needed for license checking that aren't in main production dependencies
     "geopandas>=0.11.1,<1.1; python_version < '3.12'",
     "geopandas>=0.13.2; python_version >= '3.12'",
-    "pyspark>=3.5.5,<4.0.0"
+    "pyspark>=3.5.5,<4.0.0",
+    "pyspark>=3.5.5,<5.0.0"
 ]
 
 [tool.poetry]