Merge pull request #1287 from datajoint/claude/drop-legacy-support-rFhLT

d-v-b · web-flow · commit 67cdb685d6fd · 2025-12-22T22:53:11.000+01:00
Drops support for Python &lt; 3.10 and MySQL &lt; 8.0
diff --git a/.github/workflows/post_draft_release_published.yaml b/.github/workflows/post_draft_release_published.yaml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         include:
-          - py_ver: "3.9"
+          - py_ver: "3.10"
     runs-on: ubuntu-latest
     env:
       PY_VER: ${{matrix.py_ver}}
@@ -40,14 +40,14 @@ jobs:
       - name: Update version.py
         run: |
           VERSION=$(echo "${{ github.event.release.name }}" | grep -oP '\d+\.\d+\.\d+')
-          sed -i "s/^__version__ = .*/__version__ = \"$VERSION\"/" datajoint/version.py
-          cat datajoint/version.py
+          sed -i "s/^__version__ = .*/__version__ = \"$VERSION\"/" src/datajoint/version.py
+          cat src/datajoint/version.py
           # Commit the changes
           BRANCH_NAME="update-version-$VERSION"
           git switch -c $BRANCH_NAME
           git config --global user.name "github-actions"
           git config --global user.email "github-actions@github.com"
-          git add datajoint/version.py
+          git add src/datajoint/version.py
           git commit -m "Update version.py to $VERSION"
           echo "BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
       - name: Update README.md badge
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -21,11 +21,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        py_ver: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        py_ver: ["3.10", "3.11", "3.12", "3.13"]
         mysql_ver: ["8.0"]
-        include:
-          - py_ver: "3.9"
-            mysql_ver: "5.7"
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{matrix.py_ver}}
diff --git a/docker-compose.yaml b/docker-compose.yaml
@@ -41,7 +41,7 @@ services:
       context: .
       dockerfile: Dockerfile
       args:
-        PY_VER: ${PY_VER:-3.9}
+        PY_VER: ${PY_VER:-3.10}
         HOST_UID: ${HOST_UID:-1000}
     depends_on:
       db:
diff --git a/docs/src/client/install.md b/docs/src/client/install.md
@@ -1,6 +1,6 @@
 # Install and Connect
 
-DataJoint is implemented for Python 3.4+.
+DataJoint is implemented for Python 3.10+.
 You may install it from [PyPI](https://pypi.python.org/pypi/datajoint):
 
 ```bash
@@ -25,7 +25,7 @@ to connect to DataJoint pipelines.
 
 Quick install steps for advanced users are as follows:
 
-- Install latest Python 3.x and ensure it is in `PATH` (3.6.3 current at time of writing)
+- Install latest Python 3.x and ensure it is in `PATH` (3.10+ required)
   ```bash
   pip install datajoint
   ```
@@ -46,7 +46,7 @@ Python for Windows is available from:
 
 https://www.python.org/downloads/windows
 
-The latest 64 bit 3.x version, currently 3.6.3, is available from the [Python site](https://www.python.org/ftp/python/3.6.3/python-3.6.3-amd64.exe).
+The latest 64 bit 3.x version (3.10 or later required) is available from the [Python site](https://www.python.org/downloads/windows/).
 
 From here run the installer to install Python.
 
diff --git a/docs/src/client/settings.md b/docs/src/client/settings.md
@@ -1,6 +1,6 @@
 # Configuration Settings
 
-DataJoint uses a strongly-typed configuration system built on [pydantic-settings](https://docs.pydantic.dev/latest/concepts/pydantic_settings/).
+DataJoint uses a type-checked configuration system built on [pydantic-settings](https://docs.pydantic.dev/latest/concepts/pydantic_settings/).
 
 ## Configuration Sources
 
diff --git a/docs/src/develop.md b/docs/src/develop.md
@@ -43,15 +43,15 @@ git clone https://github.com/datajoint/datajoint-python.git
 ### With Virtual Environment
 
 ```bash
-# Check if you have Python 3.9 or higher, if not please upgrade
+# Check if you have Python 3.10 or higher, if not please upgrade
 python --version
 # Create a virtual environment with venv
 python -m venv .venv
 source .venv/bin/activate
 pip install -e .[dev]
 
 # Or create a virtual environment with conda
-conda create -n dj python=3.13 # any 3.9+ is fine
+conda create -n dj python=3.13 # any 3.10+ is fine
 conda activate dj
 pip install -e .[dev]
 ```
@@ -81,7 +81,7 @@ Here are some options that provide a great developer experience:
   - Ensure you have [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
   - Ensure you have [Docker](https://docs.docker.com/get-docker/)
   - `git clone` the codebase repository and open it in VSCode
-  - Issue the following command in the terminal to build and run the Docker container: `HOST_UID=$(id -u) PY_VER=3.11 DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py) docker compose --profile test run --rm -it djtest -- sh -c 'pip install -qe ".[dev]" && bash'`
+  - Issue the following command in the terminal to build and run the Docker container: `HOST_UID=$(id -u) PY_VER=3.11 DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' src/datajoint/version.py) docker compose --profile test run --rm -it djtest -- sh -c 'pip install -qe ".[dev]" && bash'`
   - Issue the following command in the terminal to stop the Docker compose stack: `docker compose --profile test down`
 
 [Back to top](#table-of-contents)
diff --git a/docs/src/quick-start.md b/docs/src/quick-start.md
@@ -12,7 +12,7 @@ Advanced users can install DataJoint locally. Please see the installation instru
 ## Installation
 
 First, please [install Python](https://www.python.org/downloads/) version
-3.8 or later.
+3.10 or later.
 
 Next, please install DataJoint via one of the following:
 
@@ -413,7 +413,7 @@ data = query.fetch(order_by='`select` desc')
 ```
 
 The `order_by` value is eventually passed to the `ORDER BY`
-[clause](https://dev.mysql.com/doc/refman/5.7/en/order-by-optimization.html).
+[clause](https://dev.mysql.com/doc/refman/8.0/en/order-by-optimization.html).
 
 ### Limiting results
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -23,7 +23,7 @@ dependencies = [
   "setuptools",
   "pydantic-settings>=2.0.0",
 ]
-requires-python = ">=3.9,<3.14"
+requires-python = ">=3.10,<3.14"
 authors = [
   {name = "Dimitri Yatsenko", email = "dimitri@datajoint.com"},
   {name = "Thinh Nguyen", email = "thinh@datajoint.com"},
@@ -102,7 +102,7 @@ dev = [
 [tool.ruff]
 # Equivalent to flake8 configuration
 line-length = 127
-target-version = "py39"
+target-version = "py310"
 
 [tool.ruff.lint]
 # Enable specific rule sets equivalent to flake8 configuration
@@ -176,7 +176,7 @@ test = { features = ["test"], solve-group = "default" }
 [tool.pixi.tasks]
 
 [tool.pixi.dependencies]
-python = ">=3.9,<3.14"
+python = ">=3.10,<3.14"
 graphviz = ">=13.1.2,<14"
 
 [tool.pixi.activation]
diff --git a/src/datajoint/condition.py b/src/datajoint/condition.py
@@ -8,7 +8,6 @@
 import re
 import uuid
 from dataclasses import dataclass
-from typing import List, Union
 
 import numpy
 import pandas
@@ -67,8 +66,8 @@ class Top:
     In SQL, this corresponds to ORDER BY ... LIMIT ... OFFSET
     """
 
-    limit: Union[int, None] = 1
-    order_by: Union[str, List[str]] = "KEY"
+    limit: int | None = 1
+    order_by: str | list[str] = "KEY"
     offset: int = 0
 
     def __post_init__(self):
diff --git a/src/datajoint/connection.py b/src/datajoint/connection.py
@@ -86,7 +86,7 @@ def conn(host=None, user=None, password=None, *, init_fun=None, reset=False, use
     :param reset: whether the connection should be reset or not
     :param use_tls: TLS encryption option. Valid options are: True (required), False
         (required no TLS), None (TLS preferred, default), dict (Manually specify values per
-        https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options).
+        https://dev.mysql.com/doc/refman/8.0/en/connection-options.html#encrypted-connection-options).
     """
     if not hasattr(conn, "connection") or reset:
         host = host if host is not None else config["database.host"]
diff --git a/src/datajoint/settings.py b/src/datajoint/settings.py
@@ -33,7 +33,7 @@
 from copy import deepcopy
 from enum import Enum
 from pathlib import Path
-from typing import Any, Dict, Iterator, Literal, Optional, Tuple, Union
+from typing import Any, Iterator, Literal
 
 from pydantic import Field, SecretStr, field_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
@@ -58,7 +58,7 @@
 logger = logging.getLogger(__name__.split(".")[0])
 
 
-def find_config_file(start: Optional[Path] = None) -> Optional[Path]:
+def find_config_file(start: Path | None = None) -> Path | None:
     """
     Search for datajoint.json in current and parent directories.
 
@@ -89,7 +89,7 @@ def find_config_file(start: Optional[Path] = None) -> Optional[Path]:
         current = current.parent
 
 
-def find_secrets_dir(config_path: Optional[Path] = None) -> Optional[Path]:
+def find_secrets_dir(config_path: Path | None = None) -> Path | None:
     """
     Find the secrets directory.
 
@@ -116,7 +116,7 @@ def find_secrets_dir(config_path: Optional[Path] = None) -> Optional[Path]:
     return None
 
 
-def read_secret_file(secrets_dir: Optional[Path], name: str) -> Optional[str]:
+def read_secret_file(secrets_dir: Path | None, name: str) -> str | None:
     """
     Read a secret value from a file in the secrets directory.
 
@@ -148,19 +148,19 @@ class DatabaseSettings(BaseSettings):
     )
 
     host: str = Field(default="localhost", validation_alias="DJ_HOST")
-    user: Optional[str] = Field(default=None, validation_alias="DJ_USER")
-    password: Optional[SecretStr] = Field(default=None, validation_alias="DJ_PASS")
+    user: str | None = Field(default=None, validation_alias="DJ_USER")
+    password: SecretStr | None = Field(default=None, validation_alias="DJ_PASS")
     port: int = Field(default=3306, validation_alias="DJ_PORT")
     reconnect: bool = True
-    use_tls: Optional[bool] = None
+    use_tls: bool | None = None
 
 
 class ConnectionSettings(BaseSettings):
     """Connection behavior settings."""
 
     model_config = SettingsConfigDict(extra="forbid", validate_assignment=True)
 
-    init_function: Optional[str] = None
+    init_function: str | None = None
     charset: str = ""  # pymysql uses '' as default
 
 
@@ -184,8 +184,8 @@ class ExternalSettings(BaseSettings):
         validate_assignment=True,
     )
 
-    aws_access_key_id: Optional[str] = Field(default=None, validation_alias="DJ_AWS_ACCESS_KEY_ID")
-    aws_secret_access_key: Optional[SecretStr] = Field(default=None, validation_alias="DJ_AWS_SECRET_ACCESS_KEY")
+    aws_access_key_id: str | None = Field(default=None, validation_alias="DJ_AWS_ACCESS_KEY_ID")
+    aws_secret_access_key: SecretStr | None = Field(default=None, validation_alias="DJ_AWS_SECRET_ACCESS_KEY")
 
 
 class Config(BaseSettings):
@@ -226,18 +226,18 @@ class Config(BaseSettings):
     fetch_format: Literal["array", "frame"] = "array"
     enable_python_native_blobs: bool = True
     add_hidden_timestamp: bool = False
-    filepath_checksum_size_limit: Optional[int] = None
+    filepath_checksum_size_limit: int | None = None
 
     # External stores configuration
-    stores: Dict[str, Dict[str, Any]] = Field(default_factory=dict)
+    stores: dict[str, dict[str, Any]] = Field(default_factory=dict)
 
     # Cache paths
-    cache: Optional[Path] = None
-    query_cache: Optional[Path] = None
+    cache: Path | None = None
+    query_cache: Path | None = None
 
     # Internal: track where config was loaded from
-    _config_path: Optional[Path] = None
-    _secrets_dir: Optional[Path] = None
+    _config_path: Path | None = None
+    _secrets_dir: Path | None = None
 
     @field_validator("loglevel", mode="after")
     @classmethod
@@ -248,13 +248,13 @@ def set_logger_level(cls, v: str) -> str:
 
     @field_validator("cache", "query_cache", mode="before")
     @classmethod
-    def convert_path(cls, v: Any) -> Optional[Path]:
+    def convert_path(cls, v: Any) -> Path | None:
         """Convert string paths to Path objects."""
         if v is None:
             return None
         return Path(v) if not isinstance(v, Path) else v
 
-    def get_store_spec(self, store: str) -> Dict[str, Any]:
+    def get_store_spec(self, store: str) -> dict[str, Any]:
         """
         Get configuration for an external store.
 
@@ -279,11 +279,11 @@ def get_store_spec(self, store: str) -> Dict[str, Any]:
             raise DataJointError(f'Missing or invalid protocol in config.stores["{store}"]')
 
         # Define required and allowed keys by protocol
-        required_keys: Dict[str, Tuple[str, ...]] = {
+        required_keys: dict[str, tuple[str, ...]] = {
             "file": ("protocol", "location"),
             "s3": ("protocol", "endpoint", "bucket", "access_key", "secret_key", "location"),
         }
-        allowed_keys: Dict[str, Tuple[str, ...]] = {
+        allowed_keys: dict[str, tuple[str, ...]] = {
             "file": ("protocol", "location", "subfolding", "stage"),
             "s3": (
                 "protocol",
@@ -311,7 +311,7 @@ def get_store_spec(self, store: str) -> Dict[str, Any]:
 
         return spec
 
-    def load(self, filename: Union[str, Path]) -> None:
+    def load(self, filename: str | Path) -> None:
         """
         Load settings from a JSON file.
 
@@ -330,7 +330,7 @@ def load(self, filename: Union[str, Path]) -> None:
         self._update_from_flat_dict(data)
         self._config_path = filepath
 
-    def _update_from_flat_dict(self, data: Dict[str, Any]) -> None:
+    def _update_from_flat_dict(self, data: dict[str, Any]) -> None:
         """Update settings from a flat dict with dot notation keys."""
         for key, value in data.items():
             parts = key.split(".")
diff --git a/src/datajoint/table.py b/src/datajoint/table.py
@@ -8,7 +8,6 @@
 import re
 import uuid
 from pathlib import Path
-from typing import Union
 
 import numpy as np
 import pandas
@@ -430,7 +429,7 @@ def delete_quick(self, get_count=False):
     def delete(
         self,
         transaction: bool = True,
-        safemode: Union[bool, None] = None,
+        safemode: bool | None = None,
         force_parts: bool = False,
         force_masters: bool = False,
     ) -> int:
